Analyze and visualize RNA-Seq data with pathlinkRUpdated 3 days ago

Andy An, Travis Blimkie

Rendered from pathlinkR.Rmd in pathlinkR 1.3.3.
Saving arrays to artifacts and back againUpdated 3 days ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.matrix 1.7.2.
Definition of binding sites from iCLIP signalUpdated 3 days ago

Mirko Brüggemann, Kathi Zarnack

Rendered from vignette.Rmd in BindingSiteFinder 2.5.2.
CleanUpRNAseq: detecting and correcting gDNA contamination in RNA-seq dataUpdated 4 days ago

Haibo Liu, Kai Hu, Kevin O'Connor, Michelle Kelliher, Lihua Julie Zhu

Rendered from CleanUpRNAseq.Rmd in CleanUpRNAseq 1.1.1.
Introduction to the SpatialFeatureExperiment classUpdated 5 days ago

Lambda Moses, Lior Pachter

Rendered from SFE.Rmd in SpatialFeatureExperiment 1.9.4.
detecting relevant genes with destiny 3Updated 6 days ago

Philipp Angerer

Rendered from Gene-Relevance.Rmd in destiny 3.21.0.
The epialleleR User's GuideUpdated 7 days ago

Oleksii Nikolaienko

Rendered from epialleleR.Rmd in epialleleR 1.15.1.
mia: Microbiome analysis toolsUpdated 9 days ago

Tuomas Borman

Rendered from mia.Rmd in mia 1.15.6.
Analyzing RNA-seq data with DESeq2Updated 9 days ago

Michael I. Love, Simon Anders, and Wolfgang Huber

Rendered from DESeq2.Rmd in DESeq2 1.47.1.
Spatial Linear and Mixed-Effects Modelling with spicyRUpdated 10 days ago

Nicolas Canete, Ellis Patrick, Alex Qin, Shreya Rao

Rendered from spicyR.Rmd in spicyR 1.19.3.
VSClust with Bioconductor objectsUpdated 10 days ago

Veit Schwämmle

Rendered from Integrate_With_Bioconductor_Objects.Rmd in vsclust 1.9.3.
VSClust workflowUpdated 10 days ago

Veit Schwämmle

Rendered from Run_VSClust_Workflow.Rmd in vsclust 1.9.3.
destiny main vignette: Start here!Updated 10 days ago

Philipp Angerer

Rendered from Diffusion-Maps.Rmd in destiny 3.21.0.
A note on fimo16 in TFutilsUpdated 11 days ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from fimo16.Rmd in TFutils 1.27.1.
Introduction to the AnVIL packageUpdated 11 days ago

Nitesh Turaga, Vincent Carey, BJ Stubbs, Marcel Ramos, Martin Morgan

Rendered from Introduction.Rmd in AnVIL 1.19.3.
The rawrr R package - Direct Access to Orbitrap Data and BeyondUpdated 12 days ago

Tobias Kockmann, Christian Panse

Rendered from rawrr.Rmd in rawrr 1.15.8.
EpiDISH - Epigenetic Dissection of Intra-Sample-HeterogeneityUpdated 12 days ago

Shijie C. Zheng, Andrew E. Teschendorff

Rendered from EpiDISH.Rmd in EpiDISH 2.23.1.
Analysis of T and B cell receptor repertoires with ClustIRRUpdated 13 days ago

Simo Kitanovski

Rendered from User_manual.Rmd in ClustIRR 1.5.13.
trackViewer Vignette: plot interaction dataUpdated 15 days ago

Jianhong Ou, Lihua Julie Zhu

Rendered from plotInteractionData.Rmd in trackViewer 1.43.1.
Brings Orbitrap Mass Spectrometry Data to Life; Fast and ColorfulUpdated 16 days ago

Christian Trachsel, Christian Panse, Tobias Kockmann

Rendered from rawDiag.Rmd in rawDiag 1.3.4.
Analyzing differential co-expression with csdRUpdated 16 days ago

Jakob Peder Pettersen

Rendered from csdR.Rmd in csdR 1.13.3.
On Using and Extending the MsBackendRawFileReader BackendUpdated 17 days ago

Tobias Kockmann, Christian Panse

Rendered from MsBackendRawFileReader.Rmd in MsBackendRawFileReader 1.13.1.
BridgeDbR TutorialUpdated 17 days ago

Egon Willighagen

Rendered from tutorial.Rmd in BridgeDbR 2.17.1.
Mass decomposition with the Rdisop packageUpdated 18 days ago

Steffen Neumann$^\dagger$, Anton Pervukhin$^\ddagger$, Sebastian Böcker$^\ddagger$, $^\dagger$Leibniz Institute of Plant Biochemistry, [email protected], $^\ddagger$Friedrich-Schiller-University Jena, [email protected], [email protected]

Rendered from Rdisop.Rmd in Rdisop 1.67.3.
autonomics: platform-aware analysisUpdated 19 days ago

Aditya Bhagwat

Rendered from autonomics_platformaware_analysis.Rmd in autonomics 1.15.10.
BiocCheck: Ensuring Bioconductor package guidelinesUpdated 22 days ago

Marcel Ramos

Rendered from BiocCheck.Rmd in BiocCheck 1.43.2.
spoon TutorialUpdated 22 days ago

Kinnary H. Shah, Boyi Guo, Stephanie C. Hicks

Rendered from spoon.Rmd in spoon 1.3.1.
Vignette 1: Getting Started with BANDLEUpdated 22 days ago

Oliver M. Crook, Lisa M. Breckels

Rendered from v01-getting-started.Rmd in bandle 1.11.0.
Vignette 2: A workflow for analysing differential localisationUpdated 22 days ago

Oliver M. Crook, Lisa M. Breckels

Rendered from v02-workflow.Rmd in bandle 1.11.0.
Classify SequencesUpdated 26 days ago

Erik Wright

Rendered from ClassifySequences.Rnw in DECIPHER 3.3.0.
Finding neighbors in high-dimensional spaceUpdated 1 months ago

Aaron Lun

Rendered from userguide.Rmd in BiocNeighbors 2.1.0.
Customizing oncoplotsUpdated 1 months ago

Anand Mayakonda

Rendered from oncoplots.Rmd in maftools 2.23.0.
Introduction to PhILRUpdated 1 months ago

Justin Silverman

Rendered from philr-intro.Rmd in philr 1.33.0.
Gene set co-regulation analysis tutorialUpdated 2 months ago

Alexey Sergushichev

Rendered from geseca-tutorial.Rmd in fgsea 1.33.0.
Using fgsea packageUpdated 2 months ago

Alexey Sergushichev

Rendered from fgsea-tutorial.Rmd in fgsea 1.33.0.
BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment testsUpdated 2 months ago

Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic Bastian

Rendered from BgeeDB_Manual.Rmd in BgeeDB 2.33.0.
pcaExplorer User GuideUpdated 2 months ago

Federico Marini, Harald Binder

Rendered from pcaExplorer.Rmd in pcaExplorer 3.1.0.
maftools : Summarize, Analyze and Visualize MAF FilesUpdated 2 months ago

Anand Mayakonda

Rendered from maftools.Rmd in maftools 2.23.0.
BatchQC ExamplesUpdated 4 months ago

W. Evan Johnson, Jessica McClintock, Solaiappan Manimaran

Rendered from BatchQC_examples.Rmd in BatchQC 2.3.0.
Introduction to BatchQCUpdated 4 months ago

W. Evan Johnson, Jessica McClintock

Rendered from BatchQC_Intro.Rmd in BatchQC 2.3.0.
recount quick start guideUpdated 6 months ago

Leonardo Collado-Torres

Rendered from recount-quickstart.Rmd in recount 1.33.0.
clusterExperiment VignetteUpdated 7 months ago

Elizabeth Purdom and Davide Risso

Rendered from clusterExperimentTutorial.Rmd in clusterExperiment 2.27.0.
Controlling bias and inflation in association studies using the empirical null distributionUpdated 7 months ago

Maarten van Iterson [aut, cre] and Erik van Zwet [ctb]

Rendered from bacon.Rmd in bacon 1.35.0.
PharmacoGx: An R Package for Analysis of Large Pharmacogenomic DatasetsUpdated 8 months ago

Petr Smirnov, Christopher Eeles, Zhaleh Safikhani, Benjamin Haibe-Kains

Rendered from CreatingPharmacoSet.Rmd in PharmacoGx 3.11.0.
Identifier mappingUpdated 8 months ago

by Alexander Pico

Rendered from Identifier-mapping.Rmd in RCy3 2.27.0.
Usage of YAPSA Updated 8 months ago

Daniel Huebschmann

Rendered from YAPSA.Rmd in YAPSA 1.33.0.
ASpliUpdated 8 months ago

Ariel Chernomoretz

Rendered from ASpli.Rnw in ASpli 2.17.0.
The RNA Centric Analysis System ReportUpdated 8 months ago

Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Altuna Akalin

Rendered from RCAS.vignette.Rmd in RCAS 1.33.0.
Characterization of miRNA and isomiR moleculesUpdated 9 months ago

Lorena Pantano

Rendered from isomiRs.Rmd in isomiRs 1.35.0.
Detection of consensus regions inside a group of experimentsUpdated 9 months ago

Astrid Deschênes, Fabien Claude Lamaze, Pascal Belleau and Arnaud Droit

Rendered from consensusSeekeR.Rmd in consensusSeekeR 1.35.0.
How to do meta-analysis of CLIP-seq peaks from multiple samples with RCASUpdated 10 months ago

Bora Uyar, Ricardo Wurmus, Altuna Akalin

Rendered from RCAS.metaAnalysis.vignette.Rmd in RCAS 1.33.0.
Vignette of the esetVis packageUpdated 11 months ago

Laure Cougnaud

Rendered from esetVis-vignette.Rmd in esetVis 1.33.0.
PureCN best practicesUpdated 12 months ago

Markus Riester

Rendered from Quick.Rmd in PureCN 2.13.0.
Overview of the PureCN R packageUpdated 12 months ago

Markus Riester

Rendered from PureCN.Rnw in PureCN 2.13.0.
ExperimentHub: Access the ExperimentHub Web ServiceUpdated 12 months ago

Bioconductor Package Maintainer

Rendered from ExperimentHub.Rmd in ExperimentHub 2.15.0.
Linnorm User ManualUpdated 1 years ago

Shun H. Yip$^{1,2,3}$, Panwen Wang$^{3}$, Jean-Pierre Kocher$^{3}$, Pak Chung Sham$^{1,4,5}$, Junwen Wang$^{3,6}$

Rendered from Linnorm_User_Manual.Rmd in Linnorm 2.31.0.
bioCancer: Interactive Multi-OMICS Cancers Data Visualization and AnalysisUpdated 1 years ago

\ Karim Mezhoud \ \ Nuclear Science Center of Tunisia, Nuclear Safety & Security Department

Rendered from bioCancer.Rmd in bioCancer 1.35.0.
Signature-specific cutoffs Updated 1 years ago

Lea Jopp-Saile and Daniel Hübschmann

Rendered from vignette_signature_specific_cutoffs.Rmd in YAPSA 1.33.0.
Confidence Intervals Updated 1 years ago

Daniel Huebschmann

Rendered from vignette_confidenceIntervals.Rmd in YAPSA 1.33.0.
Stratified Analysis of Mutational Signatures Updated 1 years ago

Daniel Huebschmann

Rendered from vignette_stratifiedAnalysis.Rmd in YAPSA 1.33.0.
Indel signature analysis Updated 1 years ago

Lea Jopp-Saile and Daniel Huebschmann

Rendered from vignettes_Indel.Rmd in YAPSA 1.33.0.
Usage of YAPSA for Whole Exome Sequencing (WES) data Updated 1 years ago

Daniel Huebschmann

Rendered from vignette_exomes.Rmd in YAPSA 1.33.0.
LC-MS/MS data processing and spectral matching workflow using msPurity and XCMSUpdated 1 years ago

Thomas N. Lawson

Rendered from msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd in msPurity 1.33.0.
ggcyto : Visualize Cytometry data with ggplotUpdated 1 years ago

Mike Jiang

Rendered from Top_features_of_ggcyto.Rmd in ggcyto 1.35.0.
Geneplast: large-scale evolutionary analysis of orthologous groups.Updated 1 years ago

Rodrigo JS Dalmolin, Sheyla Trefflich, Diego AA Morais, Mauro AA Castro.

Rendered from geneplast.Rmd in geneplast 1.33.0.
DEBrowser user guideUpdated 1 years ago

Alper Kucukural, Onur Yukselen, Manuel Garber

Rendered from DEBrowser.Rmd in debrowser 1.35.0.
SC3 package manualUpdated 2 years ago

Vladimir Kiselev

Rendered from SC3.Rmd in SC3 1.35.0.
CrispRVariants User GuideUpdated 2 years ago

Helen Lindsay, Mark Robinson

Rendered from user_guide.Rmd in CrispRVariants 1.35.0.
Detecting Drug Synergy and Antagonism with PharmacoGx 3.0+Updated 2 years ago

Christopher Eeles, Feifei Li, Petr Smirnov, Benjamin Haibe-Kains

Rendered from DetectingDrugSynergyAndAntagonism.Rmd in PharmacoGx 3.11.0.
PharmacoGx: An R Package for Analysis of Large Pharmacogenomic DatasetsUpdated 2 years ago

Petr Smirnov, Christopher Eeles, Zhaleh Safikhani, Benjamin Haibe-Kains

Rendered from PharmacoGx.Rmd in PharmacoGx 3.11.0.
Up and running with r Biocpkg("pcaExplorer")Updated 2 years ago

Federico Marini, Harald Binder

Rendered from upandrunning.Rmd in pcaExplorer 3.1.0.
IntroductionUpdated 2 years ago

Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli

Rendered from v1_introduction.Rmd in OncoScore 1.35.0.
Running OncoScoreUpdated 2 years ago

Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli

Rendered from v2_running_OncoScore.Rmd in OncoScore 1.35.0.
ROTS: Reproducibility Optimized Test StatisticUpdated 2 years ago

Tomi Suomi

Rendered from ROTS.Rnw in ROTS 1.35.0.
ExpressionAtlas package vignetteUpdated 2 years ago

Maria Keays

Rendered from ExpressionAtlas.Rmd in ExpressionAtlas 1.35.0.
Uniquorn vignetteUpdated 2 years ago

Raik Otto

Rendered from Uniquorn.Rmd in Uniquorn 2.27.0.
GenVisR: An introductionUpdated 2 years ago

Zachary Skidmore

Rendered from Intro.Rmd in GenVisR 1.39.0.
XCMS Parameter Optimization with IPOUpdated 2 years ago

Gunnar Libiseller, Thomas RiebenbauerJOANNEUM RESEARCH Forschungsgesellschaft m.b.H., Graz, Austria

Rendered from IPO.Rmd in IPO 1.33.0.
biosigner: A new method for signature discovery from omics dataUpdated 2 years ago

Philippe Rinaudo and Etienne Thevenot

Rendered from biosigner-vignette.Rmd in biosigner 1.35.0.
Copy number analysisUpdated 3 years ago

Anand Mayakonda

Rendered from cnv_analysis.Rmd in maftools 2.23.0.
Jupyter Bridge and RCy3Updated 3 years ago

by Yihang Xin and Alexander Pico

Rendered from Jupyter-bridge-rcy3.Rmd in RCy3 2.27.0.
Personlaized cancer reportUpdated 3 years ago

Anand Mayakonda

Rendered from cancer_hotspots.Rmd in maftools 2.23.0.
Introduction using limma or edgeRUpdated 3 years ago

Shian Su

Rendered from limma_edger.Rmd in Glimma 2.17.0.
Single Cells with edgeRUpdated 3 years ago

Shian Su

Rendered from single_cell_edger.Rmd in Glimma 2.17.0.
Single-cell analysis toolkit for expression in RUpdated 3 years ago

Davis McCarthy, Aaron Lun

Rendered from overview.Rmd in scater 1.35.0.
Importing transcript abundance with tximportUpdated 3 years ago

Michael I. Love, Charlotte Soneson, Mark D. Robinson

Rendered from tximport.Rmd in tximport 1.35.0.
Pigengene: Computing and using eigengenesUpdated 3 years ago

Habil Zare

Rendered from Pigengene_inference.Rnw in Pigengene 1.33.0.
Adding a new type of data to MultiDataSet objectsUpdated 3 years ago

Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González

Rendered from MultiDataSet_Extending_Proteome.Rmd in MultiDataSet 1.35.0.
Using msPurity for Precursor Ion Purity Assessments, Data Processing and Metabolite Annotation of Mass Spectrometry Fragmentation DataUpdated 3 years ago

Thomas N. Lawson

Rendered from msPurity-vignette.Rmd in msPurity 1.33.0.
Cancer networks and dataUpdated 3 years ago

by Alexander Pico

Rendered from Cancer-networks-and-data.Rmd in RCy3 2.27.0.
DESeq2Updated 3 years ago

Shian Su

Rendered from DESeq2.Rmd in Glimma 2.17.0.
Discovery, Identification, and Screening of Lipids and Oxylipins in HPLC-MS Datasets Using LOBSTAHSUpdated 3 years ago

James Collins

Rendered from LOBSTAHS.Rmd in LOBSTAHS 1.33.0.
Introduction to ExperimentHubDataUpdated 3 years ago

Valerie Obenchain

Rendered from ExperimentHubData.Rmd in ExperimentHubData 1.33.0.
Pedigree Analysis and Familial AggregationUpdated 4 years ago

Johannes Rainer

Rendered from FamAgg.Rmd in FamAgg 1.35.0.
Using scran to analyze single-cell RNA-seq dataUpdated 4 years ago

Aaron Lun

Rendered from scran.Rmd in scran 1.35.0.
Classes for genomic interaction dataUpdated 4 years ago

Aaron Lun

Rendered from interactions.Rmd in InteractionSet 1.35.0.
How to import Cytobank into a GatingSetUpdated 4 years ago

Mike Jiang

Rendered from cytobank2GatingSet.Rmd in CytoML 2.19.0.
Prepare input data for CINdexUpdated 4 years ago

Yuriy Gusev

Rendered from PrepareInputData.Rmd in CINdex 1.35.0.
How to obtain Cytoband and Stain InformationUpdated 4 years ago

Yuriy Gusev

Rendered from HowToDownloadCytobandInfo.Rmd in CINdex 1.35.0.
Cross-Platform Meta AnalysisUpdated 4 years ago

Alex Pickering

Rendered from crossmeta-vignette.Rmd in crossmeta 1.33.0.
methylKit: User Guide vr packageVersion('methylKit')Updated 4 years ago

Altuna Akalin^[Author of the vignette. See Acknowledgements for a list of contributors.] [email protected]

Rendered from methylKit.Rmd in methylKit 1.33.0.
BioQC Algorithm: Speeding up the Wilcoxon-Mann-Whitney TestUpdated 4 years ago

Gregor Sturm and Jitao David Zhang

Rendered from bioqc-efficiency.Rmd in BioQC 1.35.0.
BioQC-benchmark: Testing Efficiency, Sensitivity and Specificity of BioQC on simulated and real-world dataUpdated 4 years ago

Jitao David Zhang

Rendered from bioqc-simulation.Rmd in BioQC 1.35.0.
BioQC-kidney: The kidney expression exampleUpdated 4 years ago

Jitao David Zhang

Rendered from BioQC.Rmd in BioQC 1.35.0.
BioQC: Detect tissue heterogeneity in gene expression dataUpdated 4 years ago

Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, and Laura Badi

Rendered from bioqc-introduction.Rmd in BioQC 1.35.0.
Comparing the Wilcoxon-Mann-Whitney to alternative statistical testsUpdated 4 years ago

Jitao David Zhang

Rendered from bioqc-wmw-test-performance.Rmd in BioQC 1.35.0.
Quality control with flowAIUpdated 4 years ago

Gianni Monaco

Rendered from flowAI.Rmd in flowAI 1.37.0.
EBSEA: Exon Based Strategy for Expression Analysis of genesUpdated 4 years ago

Arfa Mehmood

Rendered from EBSEA.Rmd in EBSEA 1.35.0.
Using DirectorUpdated 4 years ago

Katherine Icay

Rendered from vignette.Rnw in Director 1.33.0.
Import FlowJo workspace to RUpdated 4 years ago

Mike Jiang

Rendered from flowjo_to_gatingset.Rmd in CytoML 2.19.0.
Usage of the recoup packageUpdated 5 years ago

Panagiotis Moulos

Rendered from recoup_intro.Rmd in recoup 1.35.0.
transcriptR: an integrative tool for ChIP- and RNA-seq based primary transcripts detection and quantificationUpdated 5 years ago

Armen R. Karapetyan, Renske A. Kuiper, Marcel W. Coolen. Department of Human Genetics, Radboud University Medical Center, The Netherlands

Rendered from transcriptR.Rmd in transcriptR 1.35.0.
Introduction to the normR packageUpdated 5 years ago

Johannes Helmuth

Rendered from normr.Rmd in normr 1.33.0.
epivizrData UsageUpdated 5 years ago

Héctor Corrada Bravo

Rendered from epivizrData.Rmd in epivizrData 1.35.0.
A quick introduction to AneuFinderUpdated 5 years ago

Aaron Taudt

Rendered from AneuFinder.Rnw in AneuFinder 1.35.0.
article frameUpdated 5 years ago

Armin Rauschenberger

Rendered from article.Rmd in globalSeq 1.35.0.
vignette frameUpdated 5 years ago

Armin Rauschenberger

Rendered from vignette.Rmd in globalSeq 1.35.0.
SMITE VignetteUpdated 5 years ago

Andrew D. Johnston, N. Ari Wijetunga, and John M. Greally

Rendered from SMITE.Rmd in SMITE 1.35.0.
How to export a GatingSet to GatingMLUpdated 5 years ago

Mike Jiang

Rendered from HowToExportGatingSet.Rmd in CytoML 2.19.0.
QUBIC TutorialUpdated 5 years ago

Yu Zhang, Juan Xie, and Qin Ma

Rendered from qubic_vignette.Rmd in QUBIC 1.35.0.
Filtering NetworksUpdated 5 years ago

Kristina Hanspers, Alexander Pico

Rendered from Filtering-Networks.Rmd in RCy3 2.27.0.
Supporting Material for Trefflich2019Updated 5 years ago

Sheyla Trefflich, Rodrigo J. S. Dalmolin, José M. Ortega, Mauro A. A. Castro.

Rendered from geneplast_Trefflich2019.Rmd in geneplast 1.33.0.
Working with Large DatasetsUpdated 5 years ago

Elizabeth Purdom and Davide Risso

Rendered from largeDataSets.Rmd in clusterExperiment 2.27.0.
pqsfinder: User GuideUpdated 5 years ago

Jiří Hon, Matej Lexa, Tomáš Martínek

Rendered from pqsfinder.Rmd in pqsfinder 2.23.0.
Overview of RCy3Updated 5 years ago

by Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Rendered from Overview-of-RCy3.Rmd in RCy3 2.27.0.
msPurity spectral database schemaUpdated 5 years ago

Thomas N. Lawson

Rendered from msPurity-spectral-database-vignette.Rmd in msPurity 1.33.0.
metaCCAUpdated 5 years ago

Anna Cichonska

Rendered from metaCCA.Rnw in metaCCA 1.35.0.
Visualize flowSet with ggcytoUpdated 6 years ago

Mike Jiang

Rendered from ggcyto.flowSet.Rmd in ggcyto 1.35.0.
Quick plot for cytometry dataUpdated 6 years ago

Mike Jiang

Rendered from autoplot.Rmd in ggcyto 1.35.0.
Phylogenetic-treesUpdated 6 years ago

Alexander Pico, Gildas Lepennetier

Rendered from Phylogenetic-trees.Rmd in RCy3 2.27.0.
iCARE Vignette Model ValidationUpdated 6 years ago

Parichoy Pal Choudhury

Rendered from vignette_model_validation.Rnw in iCARE 1.35.0.
CONFESSUpdated 6 years ago

Diana LOW, Efthymios MOTAKIS

Rendered from vignette.Rmd in CONFESS 1.35.0.
Using MGFRUpdated 6 years ago

Khadija El Amrani

Rendered from MGFR.Rnw in MGFR 1.33.0.
vignette sourceUpdated 6 years ago

Armin Rauschenberger

Rendered from globalSeq.Rnw in globalSeq 1.35.0.
iCARE VignetteUpdated 6 years ago

Parichoy Pal Choudhury

Rendered from vignette.Rnw in iCARE 1.35.0.
Custom Graphics and LabelsUpdated 6 years ago

Kristina Hanspers, Alexander Pico

Rendered from Custom-Graphics.Rmd in RCy3 2.27.0.
Introduction to dada2Updated 6 years ago

Benjamin J Callahan, Joey McMurdie, Susan Holmes

Rendered from dada2-intro.Rmd in dada2 1.35.0.
QuaternaryProdUpdated 6 years ago

Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam

Rendered from QuaternaryProdVignette.Rmd in QuaternaryProd 1.41.0.
OPPAR: Outlier Profile and Pathway Analysis in RUpdated 6 years ago

Soroor Hediyehzadeh

Rendered from oppar.Rmd in oppar 1.35.0.
CINdex TutorialUpdated 6 years ago

Yuriy Gusev

Rendered from CINdex.Rnw in CINdex 1.35.0.
Introduction to cellity: Classification of low quality cells in scRNA-seq data using RUpdated 6 years ago

Tomislav Ilicic & Davis McCarthy

Rendered from cellity_vignette.Rmd in cellity 1.35.0.
switchde: inference of switch-like gene behaviour along single-cell trajectoriesUpdated 6 years ago

Kieran Campbell

Rendered from switchde_vignette.Rmd in switchde 1.33.0.
Using SIGHTS R-packageUpdated 6 years ago

Elika Garg, Carl Murie and Robert Nadon

Rendered from sights.Rmd in sights 1.33.0.
__MethPed__A DNA Methylation Classifier Tool for the Identification of Pediatric Brain Tumor SubtypesUpdated 6 years ago

*Mohammad Tanvir Ahamed, Anna Danielsson, Szilárd Nemes and Helena Carén*University of Gothenburg, Sweden

Rendered from MethPed-vignette.Rmd in MethPed 1.35.0.
MergeomicsUpdated 6 years ago

Zeyneb Kurt

Rendered from Mergeomics.Rnw in Mergeomics 1.35.0.
GRmetrics: an R package for calculation and visualization of dose-response metrics based on growth rate inhibitionUpdated 6 years ago

Nicholas Clark

Rendered from GRmetrics-vignette.Rmd in GRmetrics 1.33.0.
GEM: fast association study for the interplay of Gene, Environment and MethylationUpdated 6 years ago

Hong Pan

Rendered from user_guide.Rmd in GEM 1.33.0.
garfield GuideUpdated 6 years ago

Valentina Iotchkova

Rendered from vignette.Rnw in garfield 1.35.0.
Bioconductor Package VignetteUpdated 6 years ago

Tsu-Pei Chiu, Federico Comoglio and Remo Rohs

Rendered from DNAshapeR.Rmd in DNAshapeR 1.35.0.
ctsGE PackageUpdated 6 years ago

Michal Sharabi-Schwager, Ron Ophir

Rendered from ctsGE.Rmd in ctsGE 1.33.0.
An Introduction to covRNAUpdated 6 years ago

Lara Urban

Rendered from covRNA.Rmd in covRNA 1.33.0.
biobroom VignetteUpdated 6 years ago

Andrew J. Bass, Emily Nelson, David Robinson and John D. Storey

Rendered from biobroom_vignette.Rmd in biobroom 1.39.0.
CellMapper VignetteUpdated 6 years ago

Brad Nelms

Rendered from CellMapper.Rnw in CellMapper 1.33.0.
Using BadRegionFinderUpdated 6 years ago

Sarah Sandmann

Rendered from BadRegionFinder.Rnw in BadRegionFinder 1.35.0.
EGSEA vignetteUpdated 6 years ago

Monther Alhamdoosh

Rendered from EGSEA.Rnw in EGSEA 1.35.0.
ClusterSignificance VignetteUpdated 6 years ago

Jesper Robert Gådin and Jason T. Serviss

Rendered from ClusterSignificance-vignette.Rmd in ClusterSignificance 1.35.0.
Cytoscape and igraphUpdated 6 years ago

by Alexander Pico

Rendered from Cytoscape-and-iGraph.Rmd in RCy3 2.27.0.
Upgrading existing scriptsUpdated 6 years ago

by Alexander Pico, Tanja Muetze, Paul Shannon

Rendered from Upgrading-existing-scripts.Rmd in RCy3 2.27.0.
Group nodesUpdated 6 years ago

by Mark Grimes

Rendered from Group-nodes.Rmd in RCy3 2.27.0.
Cytoscape and NDExUpdated 6 years ago

by Alexander Pico, Florian Auer

Rendered from Cytoscape-and-NDEx.Rmd in RCy3 2.27.0.
Network functions and visualizationUpdated 6 years ago

by Alexander Pico

Rendered from Network-functions-and-visualization.Rmd in RCy3 2.27.0.
Cytoscape and graphNELUpdated 6 years ago

by Alexander Pico

Rendered from Cytoscape-and-graphNEL.Rmd in RCy3 2.27.0.
Importing dataUpdated 6 years ago

by Alexander Pico

Rendered from Importing-data.Rmd in RCy3 2.27.0.
QSEA TutorialUpdated 6 years ago

Matthias Lienhard, Lukas Chavez and Ralf Herwig

Rendered from qsea_tutorial.Rmd in qsea 1.33.0.
A Guide to multiClustUpdated 6 years ago

Nathan Lawlor

Rendered from multiClust.Rmd in multiClust 1.37.0.
waterfall: function introductionUpdated 7 years ago

Zachary Skidmore

Rendered from waterfall_introduction.Rmd in GenVisR 1.39.0.
RImmPort: Enabling ready-for-analysis immunology research dataUpdated 7 years ago

Ravi Shankar

Rendered from RImmPort_Article.Rmd in RImmPort 1.35.0.
RImmPort: Quick Start GuideUpdated 7 years ago

Ravi Shankar

Rendered from RImmPort_QuickStart.Rmd in RImmPort 1.35.0.
Introduction to MultiDataSetUpdated 7 years ago

| Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain | Bioinformatics Research Group in Epidemiology | (http://www.creal.cat/brge.htm)

Rendered from MultiDataSet.Rmd in MultiDataSet 1.35.0.
Differential gene expression data formats converterUpdated 7 years ago

Andrzej Oleś

Rendered from DEFormats.Rmd in DEFormats 1.35.0.
SNPediaRUpdated 7 years ago

David Montaner

Rendered from SNPediaR.Rmd in SNPediaR 1.33.0.
Analysing Ribo-Seq data with the "RiboProfiling" packageUpdated 7 years ago

A. Popa

Rendered from RiboProfiling.Rnw in RiboProfiling 1.37.0.
Introduction to epivizrStandaloneUpdated 7 years ago

Héctor Corrada Bravo

Rendered from EpivizrStandalone.Rmd in epivizrStandalone 1.35.0.
MetaboSignal 2: merging KEGG with additional interaction resourcesUpdated 7 years ago

Andrea Rodriguez-Martinez

Rendered from MetaboSignal2.Rmd in MetaboSignal 1.37.0.
Generate synthetic nucleosome mapsUpdated 7 years ago

Astrid Deschênes

Rendered from nucleoSim.Rmd in nucleoSim 1.35.0.
Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq packageUpdated 7 years ago

Malgorzata Nowicka

Rendered from DRIMSeq.Rnw in DRIMSeq 1.35.0.
Workflow exampleUpdated 7 years ago

Christian Arnold, Pooja Bhat, Judith Zaugg

Rendered from workflow.Rmd in SNPhood 1.37.0.
Anaquin - VignetteUpdated 7 years ago

Ted Wong ([email protected])

Rendered from Anaquin.Rmd in Anaquin 2.31.0.
Using BioQC with signed genesetsUpdated 7 years ago

Jitao David Zhang and Gregor Sturm

Rendered from bioqc-signedGenesets.Rmd in BioQC 1.35.0.
Analysis of high-throughput sequencing of T and B cell receptors with LymphoSeqUpdated 8 years ago

David G. Coffey, MD

Rendered from LymphoSeq.Rmd in LymphoSeq 1.35.0.
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysisUpdated 8 years ago

Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos

Rendered from CHRONOS.Rmd in CHRONOS 1.35.0.
Combination Connectivity MappingUpdated 8 years ago

Alex Pickering

Rendered from ccmap-vignette.Rmd in ccmap 1.33.0.
General ManualUpdated 8 years ago

Karen Y. Orostica

Rendered from chromPlot.Rnw in chromPlot 1.35.0.
Introduction to lpsymphonyUpdated 8 years ago

Vladislav Kim

Rendered from lpsymphony.Rnw in lpsymphony 1.35.0.
covEBUpdated 8 years ago

C. Pacini

Rendered from covEB.Rnw in covEB 1.33.0.
Pairwise interaction testsUpdated 8 years ago

Mathieu Emily

Rendered from GenePair.Rnw in GeneGeneInteR 1.33.0.
Usage of AMOUNTAINUpdated 8 years ago

Dong Li [email protected]

Rendered from AMOUNTAIN.Rmd in AMOUNTAIN 1.33.0.
subSeq ExampleUpdated 8 years ago

Andrew J. Bass

Rendered from subSeq.Rnw in subSeq 1.37.0.
geneAttribution: Identification of Candidate Genes Associated with Noncoding Genetic VariationUpdated 8 years ago

Arthur Wuster

Rendered from geneAttribution.Rmd in geneAttribution 1.33.0.
splineTimeRUpdated 8 years ago

Herbert Braselmann

Rendered from splineTimeR.Rnw in splineTimeR 1.35.0.
Introduction to Independent Hypothesis Weighting with the IHW PackageUpdated 8 years ago

Nikos Ignatiadis, Wolfgang Huber

Rendered from introduction_to_ihw.Rmd in IHW 1.35.0.
GApredictionUpdated 8 years ago

Jon Bohlin

Rendered from GAprediction.Rmd in GAprediction 1.33.0.
epivizrServer UsageUpdated 8 years ago

Hector Corrada Bravo

Rendered from epivizrServer.Rmd in epivizrServer 1.35.0.
networkBMAUpdated 8 years ago

William Chad Young

Rendered from BayesKnockdown.rnw in BayesKnockdown 1.33.0.
Basic DESeq2 results explorationUpdated NaN years ago

Leonardo Collado-Torres

Rendered from SRP009615-results.Rmd in recount 1.33.0.
Design Group-Specific FISH ProbesUpdated 26 days ago

Erik Wright

Rendered from DesignProbes.Rnw in DECIPHER 3.3.0.
Design Group-Specific PrimersUpdated 26 days ago

Erik Wright

Rendered from DesignPrimers.Rnw in DECIPHER 3.3.0.
Design Microarray ProbesUpdated 26 days ago

Erik Wright

Rendered from DesignMicroarray.Rnw in DECIPHER 3.3.0.
Design Primers That Yield Group-Specific SignaturesUpdated 26 days ago

Erik Wright

Rendered from DesignSignatures.Rnw in DECIPHER 3.3.0.
Detecting Obscure Tandem Repeats in SequencesUpdated 26 days ago

Erik Wright

Rendered from RepeatRepeat.Rnw in DECIPHER 3.3.0.
Finding Chimeric SequencesUpdated 26 days ago

Erik Wright

Rendered from FindChimeras.Rnw in DECIPHER 3.3.0.
Growing Phylogenetic Trees with TreelineUpdated 26 days ago

Erik Wright

Rendered from GrowingTrees.Rnw in DECIPHER 3.3.0.
Upsize Your Clustering with ClusterizeUpdated 26 days ago

Erik Wright

Rendered from ClusteringSequences.Rnw in DECIPHER 3.3.0.
iSEEtree: interactive exploration of microbiome dataUpdated 26 days ago

Giulio Benedetti

Rendered from iSEEtree.Rmd in iSEEtree 1.1.0.
From functional enrichment results to biological networksUpdated 26 days ago

Astrid Deschênes, Pascal Belleau, Robert L Faure and Maria J Fernandes

Rendered from enrichViewNet.Rmd in enrichViewNet 1.5.0.
Introduction to SurfRUpdated 26 days ago

Aurora Maurizio, Anna Sofia Tascini, and Marco Jacopo Morelli

Rendered from Intro_to_SurfR.Rmd in SurfR 1.3.1.
Introduction to the transomics2cytoscape packageUpdated 26 days ago

by Kozo Nishida, Katsuyuki Yugi

Rendered from transomics2cytoscape.Rmd in transomics2cytoscape 1.17.0.
destiny 2.0 brought the Diffusion Pseudo Time (DPT) classUpdated 26 days ago

Philipp Angerer

Rendered from DPT.Rmd in destiny 3.21.0.
The effects of a global vs. local kernelUpdated 26 days ago

Philipp Angerer

Rendered from Global-Sigma.Rmd in destiny 3.21.0.
tidyverse and ggplot integration with destinyUpdated 26 days ago

Philipp Angerer

Rendered from tidyverse.Rmd in destiny 3.21.0.
Cancer Testis explorerUpdated 27 days ago

Julie Devis, Laurent Gatto, Axelle Loriot

Rendered from CTexploreR.Rmd in CTexploreR 1.3.0.
gDR annotationUpdated 27 days ago

gDR team

Rendered from gDR-annotation.Rmd in gDRcore 1.5.2.
Using SingleR to annotate single-cell RNA-seq dataUpdated 28 days ago

Aaron Lun, Jared M. Andrews, Friederike Dündar, Daniel Bunis

Rendered from SingleR.Rmd in SingleR 2.9.1.
segmentSeq: small RNA locus detectionUpdated 28 days ago

Samuel Granjeaud

Rendered from segmentSeq.Rnw in segmentSeq 2.41.0.
Cardinal 3: User guide for mass spectrometry imaging analysisUpdated 28 days ago

Kylie Ariel Bemis

Rendered from Cardinal3-guide.Rmd in Cardinal 3.9.0.
baySeqUpdated 28 days ago

Samuel Granjeaud

Rendered from baySeq.Rnw in baySeq 2.41.0.
Assessing Differential Gene Expression Experiments with the erccdashboardUpdated 29 days ago

Sarah Munro, Steve Lund

Rendered from erccdashboard.Rmd in erccdashboard 1.41.0.
segmentsSeq: Methylation locus identificationUpdated 29 days ago

Samuel Granjeaud

Rendered from methylationAnalysis.Rnw in segmentSeq 2.41.0.
Creating new MsBackend classesUpdated 30 days ago

RforMassSpectrometry Package Maintainer

Rendered from MsBackend.Rmd in Spectra 1.17.1.
Getting Started with scDiagnosticsUpdated 30 days ago

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered from scDiagnostics.Rmd in scDiagnostics 1.1.0.
Visualization of Cell Type AnnotationsUpdated 30 days ago

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered from VisualizationTools.Rmd in scDiagnostics 1.1.0.
Evaluation of Dataset and Marker Gene AlignmentUpdated 30 days ago

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered from DatasetMarkerGeneAlignment.Rmd in scDiagnostics 1.1.0.
Detection and Analysis of Annotation AnomaliesUpdated 30 days ago

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered from AnnotationAnomalies.Rmd in scDiagnostics 1.1.0.
AnVILWorkflow: Run batch analysis workflows including non-R tools leveraing Cloud resourcesUpdated 30 days ago

Sehyun Oh

Rendered from salmon.Rmd in AnVILWorkflow 1.7.1.
Differential Allelic Representation (DAR) analysisUpdated 1 months ago

Lachlan Baer, Stevie Pederson

Rendered from dar.Rmd in tadar 1.5.0.
Integrate miRNA and gene expression data with MIRitUpdated 1 months ago

Jacopo Ronchi

Rendered from MIRit.Rmd in MIRit 1.3.0.
scoup: Simulate Codons with Darwinian Selection Incorporated as an Ornstein-Uhlenbeck ProcessUpdated 1 months ago

Hassan Sadiq

Rendered from scoup.Rmd in scoup 1.1.0.
StatialUpdated 1 months ago

Farhan Ameen, Sourish Iyengar, Alex Qin, Ellis Patrick

Rendered from Statial.Rmd in Statial 1.9.0.
Mutational Signature Comprehensive Analysis ToolkitUpdated 1 months ago

Aaron Chevalier, Joshua Campbell

Rendered from musicatk.Rmd in musicatk 2.1.0.
Accurate Inference of Genetic Ancestry from Cancer-derived SequencesUpdated 1 months ago

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Rendered from RAIDS.Rmd in RAIDS 1.5.0.
OmicsMLRepoR - QuickstartUpdated 1 months ago

Sehyun Oh, Kaelyn Long

Rendered from Quickstart.Rmd in OmicsMLRepoR 1.1.0.
Running an AnVIL workflow within RUpdated 1 months ago

Kayla Interdonato, Yubo Cheng, Martin Morgan

Rendered from RunningWorkflow.Rmd in AnVIL 1.19.3.
Introduction to the AnVILAz packageUpdated 1 months ago

Marcel Ramos, Martin Morgan

Rendered from IntroductionToAnVILAz.Rmd in AnVILAz 1.1.0.
Working with workspaces on AnVIL AzureUpdated 1 months ago

Marcel Ramos, Martin Morgan

Rendered from AnVILAzWorkspaces.Rmd in AnVILAz 1.1.0.
Working with AnVIL on GCPUpdated 1 months ago

Nitesh Turaga, Vincent Carey, BJ Stubbs, Marcel Ramos, Martin Morgan

Rendered from AnVILGCPIntroduction.Rmd in AnVILGCP 1.1.1.
An introduction to the SingleCellAlleleExperiment classUpdated 1 months ago

Jonas Schuck, Ahmad Al Ajami, Federico Marini, Katharina Imkeller

Rendered from scae_intro.Rmd in SingleCellAlleleExperiment 1.3.0.
bioassayR Introduction and ExamplesUpdated 1 months ago

Authors: Tyler Backman, Thomas Girke

Rendered from bioassayR.Rmd in bioassayR 1.45.0.
plyxp Usage GuideUpdated 1 months ago

Justin Landis, Michael Love

Rendered from plyxp.Rmd in plyxp 1.1.0.
GSVA: gene set variation analysisUpdated 1 months ago

Robert Castelo, Axel Klenk, Justin Guinney

Rendered from GSVA.Rmd in GSVA 2.1.1.
ANCOM TutorialUpdated 1 months ago

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered from ANCOM.Rmd in ANCOMBC 2.9.0.
ANCOM-BC TutorialUpdated 1 months ago

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered from ANCOMBC.Rmd in ANCOMBC 2.9.0.
ANCOM-BC2 TutorialUpdated 1 months ago

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered from ANCOMBC2.Rmd in ANCOMBC 2.9.0.
SECOM TutorialUpdated 1 months ago

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered from SECOM.Rmd in ANCOMBC 2.9.0.
Tutorial on Data Sanity and Integrity ChecksUpdated 1 months ago

Menglu Liang$^1$, Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered from data_sanity_check.Rmd in ANCOMBC 2.9.0.
Workflow Demonstration for Deep characterization of cancer drugsUpdated 1 months ago

Trinh Nguyen

Rendered from DeepTarget_Vignette.Rmd in DeepTarget 1.1.0.
Mixed effect models for Milo DA testingUpdated 1 months ago

Mike Morgan

Rendered from milo_glmm.Rmd in miloR 2.3.0.
DirichletMultinomial for Clustering and Classification of Microbiome DataUpdated 1 months ago

Martin Morgan

Rendered from DirichletMultinomial.Rmd in DirichletMultinomial 1.49.0.
CoSIA, an R package for Cross Species Investigation and AnalysisUpdated 1 months ago

Anisha Haldar, Vishal H. Oza, Nathaniel DeVoss, Amanda D. Clark, Brittany N. Lasseigne

Rendered from CoSIA_Intro.Rmd in CoSIA 1.7.0.
Searching biological sequencesUpdated 1 months ago

Erik Wright

Rendered from SearchForResearch.Rnw in DECIPHER 3.3.0.
Annotation of mixtures of standardsUpdated 1 months ago

Gavin Rhys Lloyd

Rendered from annotate_mixtures.Rmd in MetMashR 1.1.0.
Exploring the MTox700+ libraryUpdated 1 months ago

Gavin Rhys Lloyd

Rendered from exploring_mtox.Rmd in MetMashR 1.1.0.
Using MetMashRUpdated 1 months ago

Gavin Rhys Lloyd

Rendered from using_MetMashR.Rmd in MetMashR 1.1.0.
Converting single-cell data structures between Bioconductor and PythonUpdated 1 months ago

Luke Zappia, Aaron Lun

Rendered from zellkonverter.Rmd in zellkonverter 1.17.0.
Differential abundance testing with MiloUpdated 1 months ago

Emma Dann, Mike Morgan

Rendered from milo_demo.Rmd in miloR 2.3.0.
Introduction to the scDblFinder packageUpdated 1 months ago

Pierre-Luc Germain, Aaron Lun

Rendered from introduction.Rmd in scDblFinder 1.21.0.
scDblFinderUpdated 1 months ago

Pierre-Luc Germain

Rendered from scDblFinder.Rmd in scDblFinder 1.21.0.
ASCAT to RaggedExperimentUpdated 1 months ago

Lydia King, Marcel Ramos

Rendered from ASCAT_to_RaggedExperiment.Rmd in RaggedExperiment 1.31.1.
VisiumIO: Import 10X Genomics Visium Experiment DataUpdated 1 months ago

Marcel Ramos

Rendered from VisiumIO.Rmd in VisiumIO 1.3.1.
TENxIO: Import Single Cell Data FilesUpdated 1 months ago

Marcel Ramos

Rendered from TENxIO.Rmd in TENxIO 1.9.3.
RaggedExperimentUpdated 1 months ago

Martin Morgan, Marcel Ramos

Rendered from RaggedExperiment.Rmd in RaggedExperiment 1.31.1.
Managing expiration of versioned subdirectoriesUpdated 1 months ago

Aaron Lun

Rendered from userguide.Rmd in dir.expiry 1.15.0.
beadarrayUpdated 1 months ago

Mark Dunning

Rendered from beadarray.Rmd in beadarray 2.57.0.
Developing packages with beachmatUpdated 1 months ago

Aaron Lun

Rendered from linking.Rmd in beachmat 2.23.1.
An Introduction to TMSigUpdated 1 months ago

Tyler J. Sagendorf

Rendered from TMSig.Rmd in TMSig 1.1.0.
CatsCradleUpdated 1 months ago

Anna Laddach and Michael Shapiro

Rendered from CatsCradle.Rmd in CatsCradle 1.1.0.
BayesSpaceUpdated 1 months ago

Edward Zhao, Matt Stone, Xing Ren, and Raphael Gottardo

Rendered from BayesSpace.Rmd in BayesSpace 1.17.0.
Dockstore and Bioconductor for AnVILUpdated 1 months ago

BJ Stubbs, S Gopaulakrishnan, Nitesh Truaga, Martin Morgan, Vincent Carey

Rendered from BiocDockstore.Rmd in AnVIL 1.19.3.
Save/load spatial omics data to/from fileUpdated 1 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.spatial 1.7.1.
Converting Common Data Formats to Phyloseq and TreeSummarizedExperimentUpdated 1 months ago

Francesc Catala-Moll

Rendered from data_import.Rmd in dar 1.3.0.
Saving SingleCellExperiments to artifacts and back againUpdated 1 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.sce 1.7.0.
FootprintCharterUpdated 1 months ago

Guido Barzaghi

Rendered from FootprintCharter.rmd in SingleMoleculeFootprinting 2.1.0.
methylation_calling_and_QCsUpdated 1 months ago

Guido Barzaghi

Rendered from methylation_calling_and_QCs.rmd in SingleMoleculeFootprinting 2.1.0.
single_molecule_sorting_by_TFUpdated 1 months ago

Guido Barzaghi

Rendered from single_molecule_sorting_by_TF.rmd in SingleMoleculeFootprinting 2.1.0.
Analysis of bead-summary dataUpdated 1 months ago

Mark Dunning

Rendered from beadsummary.Rmd in beadarray 2.57.0.
Motif Analysis Using motifTestRUpdated 1 months ago

Stevie Pederson

Rendered from motifAnalysis.Rmd in motifTestR 1.3.1.
Using wrappper functionsUpdated 1 months ago

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Rendered from Wrappers.Rmd in RAIDS 1.5.0.
Rsubread VignetteUpdated 1 months ago

Wei Shi

Rendered from Rsubread.Rnw in Rsubread 2.21.1.
MSstats: End to End WorkflowUpdated 1 months ago

Meena Choi

Rendered from MSstatsWorkflow.Rmd in MSstats 4.15.0.
CQN (Conditional Quantile Normalization)Updated 1 months ago

Kasper Daniel Hansen

Rendered from cqn.Rnw in cqn 1.53.0.
MOSClip vignetteUpdated 1 months ago

Paolo Martini

Rendered from mosclip_vignette.Rmd in MOSClip 1.1.0.
geomeTriD Vignette: Plot data in 3DUpdated 1 months ago

Jianhong Ou

Rendered from geomeTriD.Rmd in geomeTriD 1.1.1.
EnrichDO: a Global Weighted Model for Disease Ontology Enrichment AnalysisUpdated 1 months ago

Liang Cheng, Haixiu Yang, Hongyu Fu

Rendered from EnrichDO.Rmd in EnrichDO 1.1.0.
Automation and Visualization of Flow Cytometry Data Analysis PipelinesUpdated 1 months ago

Philippe Hauchamps, Laurent Gatto

Rendered from CytoPipeline.Rmd in CytoPipeline 1.7.0.
ontoProc: Ontology interfaces for Bioconductor, with focus on cell type identificationUpdated 1 months ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from ontoProc.Rmd in ontoProc 2.1.1.
DuplexDiscovereR tutorialUpdated 1 months ago

Egor Semenchenko

Rendered from DuplexDiscovereR.Rmd in DuplexDiscovereR 1.1.0.
D. Benchmarking with ProteinGymUpdated 1 months ago

Martin Morgan

Rendered from benchmarking.Rmd in AlphaMissenseR 1.3.0.
E. Issues & SolutionsUpdated 1 months ago

Martin Morgan

Rendered from issues.Rmd in AlphaMissenseR 1.3.0.
SpaNorm: Spatially aware library size normalisationUpdated 1 months ago

Dharmesh D. Bhuva and Agus Salim

Rendered from SpaNorm.Rmd in SpaNorm 1.1.0.
Explore Human BioMolecular Atlas Program Data PortalUpdated 1 months ago

Christine Hou

Rendered from hubmapr_vignettes.Rmd in HuBMAPR 1.1.4.
Overview of the sccomp packageUpdated 1 months ago

Stefano Mangiola

Rendered from introduction.Rmd in sccomp 1.11.0.
Introduction_1_loadmetadataUpdated 1 months ago

Hangjia Zhao

Rendered from Introduction_1_loadmetadata.Rmd in pgxRpi 1.3.0.
Introduction_3_loadfrequencyUpdated 1 months ago

Hangjia Zhao

Rendered from Introduction_3_loadfrequency.Rmd in pgxRpi 1.3.0.
Introduction_4_process_pgxsegUpdated 1 months ago

Hangjia Zhao

Rendered from Introduction_4_process_pgxseg.Rmd in pgxRpi 1.3.0.
mixOmics vignetteUpdated 1 months ago

Kim-Anh Le Cao

Rendered from vignette.Rmd in mixOmics 6.31.0.
BiocFileCache: Managing File Resources Across SessionsUpdated 1 months ago

Lori Shepherd

Rendered from BiocFileCache.Rmd in BiocFileCache 2.15.0.
The epialleleR output valuesUpdated 1 months ago

Oleksii Nikolaienko

Rendered from values.Rmd in epialleleR 1.15.1.
The GeDi User's GuideUpdated 1 months ago

Annekathrin Silvia Nedwed, Federico Marini

Rendered from GeDi_manual.Rmd in GeDi 1.3.0.
Pedigree plotting detailsUpdated 2 months ago

TM Therneau, JP Sinnwell, Louis Le Nézet

Rendered from pedigree_plot.Rmd in Pedixplorer 1.3.0.
Basic usage of GBScleanRUpdated 2 months ago

Tomoyuki Furuta, Institute of Plant Science and Resources, Okayama University, Okayama, Japan, [email protected]

Rendered from BasicUsageOfGBScleanR.rmd in GBScleanR 2.1.1.
owlents: using OWL directly in ontoProcUpdated 2 months ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from owlents.Rmd in ontoProc 2.1.1.
Introduction to Clustering of Local Indicators of Spatial Assocation (LISA) curvesUpdated 2 months ago

Nicolas Canete, Ellis Patrick, Alex Run Qin

Rendered from lisaClust.Rmd in lisaClust 1.15.6.
EpipwRUpdated 2 months ago

Jackson Barth

Rendered from EpipwR.Rmd in EpipwR 1.1.0.
An introduction to the iSEE interfaceUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from basic.Rmd in iSEE 2.19.0.
Sharing information across iSEE panelsUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from links.Rmd in iSEE 2.19.0.
Configuring iSEE appsUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from configure.Rmd in iSEE 2.19.0.
Describing the ExperimentColorMap classUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from ecm.Rmd in iSEE 2.19.0.
Deploying custom panels in the iSEE interfaceUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from custom.Rmd in iSEE 2.19.0.
How to use iSEE with big dataUpdated 2 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from bigdata.Rmd in iSEE 2.19.0.
Identification and classification of duplicated genesUpdated 2 months ago

Fabricio Almeida-Silva, Yves Van de Peer

Rendered from doubletrouble_vignette.Rmd in doubletrouble 1.7.0.
tripr User GuideUpdated 2 months ago

Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis E. Psomopoulos

Rendered from tripr_guide.Rmd in tripr 1.13.0.
Differential state analysis with muscatUpdated 2 months ago

Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Mark D Robinson

Rendered from analysis.Rmd in muscat 1.21.0.
Simulating complex design scRNA-seq data with muscatUpdated 2 months ago

Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Mark D Robinson

Rendered from simulation.Rmd in muscat 1.21.0.
Differential detection analysisUpdated 2 months ago

Jeroen Gilis, Helena L Crowell, Davide Risso, Lieven Clement

Rendered from detection.Rmd in muscat 1.21.0.
Prostar user manualUpdated 2 months ago

Samuel Wieczorek, Thomas Burger

Rendered from Prostar_UserManual.Rmd in Prostar 1.39.0.
Pedigree alignment detailsUpdated 2 months ago

TM Therneau

Rendered from pedigree_alignment.Rmd in Pedixplorer 1.3.0.
Pedigree kinship() detailsUpdated 2 months ago

TM Therneau

Rendered from pedigree_kinship.Rmd in Pedixplorer 1.3.0.
Pedigree objectUpdated 2 months ago

Terry Therneau, Elizabeth Atkinson, Louis Le Nézet

Rendered from pedigree_object.Rmd in Pedixplorer 1.3.0.
Pedixplorer tutorialUpdated 2 months ago

Louis Le Nézet

Rendered from Pedixplorer.Rmd in Pedixplorer 1.3.0.
ChIPseeker: an R package for ChIP peak Annotation, Comparison and VisualizationUpdated 2 months ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from ChIPseeker.Rmd in ChIPseeker 1.43.0.
Implementing custom iSEEindex resourcesUpdated 2 months ago

Kevin Rue-Albrecht

Rendered from resources.Rmd in iSEEindex 1.5.0.
The iSEEfier User's GuideUpdated 2 months ago

Najla Abassi, Federico Marini

Rendered from iSEEfier_userguide.Rmd in iSEEfier 1.3.0.
On-target and off-target scoring for CRISPR gRNAsUpdated 2 months ago

Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht

Rendered from crisprScore.Rmd in crisprScore 1.11.0.
Single Cell Proteomics data modellingUpdated 2 months ago

Laurent Gatto, Christophe Vanderaa

Rendered from scp_data_modelling.Rmd in scp 1.17.0.
Introduction to rhinotypeRUpdated 2 months ago

Martha Luka

Rendered from rhinotypeR.Rmd in rhinotypeR 1.1.0.
Supervised Demultiplexing using Cell Hashing and SNPsUpdated 2 months ago

Michael Lynch, Aedin Culhane

Rendered from supervised_demultiplexing.Rmd in demuxSNP 1.5.0.
Description and usage of Spectra objectsUpdated 2 months ago

RforMassSpectrometry Package Maintainer

Rendered from Spectra.Rmd in Spectra 1.17.1.
BiocFileCache Use CasesUpdated 2 months ago

Lori Shepherd

Rendered from BiocFileCache_UseCases.Rmd in BiocFileCache 2.15.0.
BiocFileCache TroubleshootingUpdated 2 months ago

Lori Shepherd

Rendered from BiocFileCache_Troubleshooting.Rmd in BiocFileCache 2.15.0.
Using methylscaper to visualize joint methylation and nucleosome occupancy dataUpdated 2 months ago

Rhonda Bacher, Parker Knight

Rendered from methylScaper.Rmd in methylscaper 1.15.0.
CBNplotUpdated 2 months ago

Noriaki Sato

Rendered from CBNplot_basic_usage.Rmd in CBNplot 1.7.0.
Damsel-workflowUpdated 2 months ago

Caitlin Page

Rendered from Damsel-workflow.Rmd in Damsel 1.3.0.
INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment AnalysisUpdated 2 months ago

Jeffrey Okamoto, Xiaoquan Wen

Rendered from INTACT.Rmd in INTACT 1.7.0.
terraTCGAdata IntroductionUpdated 2 months ago

Marcel Ramos

Rendered from terraTCGAdata.Rmd in terraTCGAdata 1.11.0.
Analyzing 3'-seq/Term-seq Data with PIPETSUpdated 2 months ago

Author: Quinlan Furumo

Rendered from PIPETS.Rmd in PIPETS 1.3.0.
Cancer Testis DatasetsUpdated 2 months ago

Julie Devis, Laurent Gatto, Axelle Loriot

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IntroductionUpdated 2 months ago

Daniele Ramazzotti, Bo Wang, Luca De Sano, Serafim Batzoglou

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Running SIMLRUpdated 2 months ago

Daniele Ramazzotti, Bo Wang, Luca De Sano, Serafim Batzoglou

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An introduction to the TRONCO R packageUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

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Data manipulationUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

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Data visualizationUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

Rendered from f3_data_visualization.Rmd in TRONCO 2.39.0.
Import/export from other toolsUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

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Loading dataUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

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Model inferenceUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

Rendered from f5_model_inference.Rmd in TRONCO 2.39.0.
Post reconstructionUpdated 2 months ago

Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti

Rendered from f6_post_reconstruction.Rmd in TRONCO 2.39.0.
xenLite: exploration of a class for Xenium demonstration dataUpdated 2 months ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from xenLite.Rmd in xenLite 1.1.0.
Using HDF5-backed matrices with beachmatUpdated 2 months ago

Aaron Lun

Rendered from userguide.Rmd in beachmat.hdf5 1.5.1.
Mass Spec Query Language Support to the Spectra PackageUpdated 2 months ago

Johannes Rainer

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Metagenomics bioinformatics at MGnifyUpdated 2 months ago

Tuomas Borman

Rendered from MGnify_course.Rmd in MGnifyR 1.3.0.
Simulating Spatial Cell-Cell Interactions Updated 2 months ago

Hechen Li

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lefser: a Megatanomic biomarker discovery toolUpdated 2 months ago

Asya Khleborodova, Sehyun Oh, Ludwig Geistlinger, and Levi Waldron

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MGnifyRUpdated 2 months ago

Tuomas Borman

Rendered from MGnifyR.Rmd in MGnifyR 1.3.0.
MGnifyR, extended vignetteUpdated 2 months ago

Tuomas Borman

Rendered from MGnifyR_long.Rmd in MGnifyR 1.3.0.
Package DetailsUpdated 2 months ago

Christian Arnold

Rendered from GRaNIE_packageDetails.Rmd in GRaNIE 1.11.0.
HoloFoodR: interface to HoloFoodR databaseUpdated 2 months ago

Tuomas Borman

Rendered from HoloFoodR.Rmd in HoloFoodR 1.1.0.
FLAMESUpdated 2 months ago

Oliver Voogd, Changqing Wang, Yupei You

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B. AlphaFold IntegrationUpdated 2 months ago

Martin Morgan

Rendered from alphafold.Rmd in AlphaMissenseR 1.3.0.
Publishing R / Bioconductor Packages To AnVIL WorkspacesUpdated 2 months ago

Martin Morgan

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Analyzing Bisulfite-seq data with dmrseqUpdated 2 months ago

Keegan Korthauer

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ClustAll User's GuideUpdated 2 months ago

Asier Ortega-Legarreta and Sara Palomino-Echeverria

Rendered from Vignette_Clustall.Rmd in ClustAll 1.3.0.
The GeneTonic User's GuideUpdated 2 months ago

Federico Marini, Annekathrin Ludt

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Scoring FunctionsUpdated 2 months ago

Reina Chau

Rendered from scoring_functions.Rmd in CaDrA 1.5.0.
ideal User's GuideUpdated 2 months ago

Federico Marini, Harald Binder

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Exploring scRNA-seq data from 5 cancer cell lines with scBubbletreeUpdated 2 months ago

Simo Kitanovski ([email protected])

Rendered from User_manual.Rmd in scBubbletree 1.9.0.
Using scrapper to analyze single-cell dataUpdated 2 months ago

Aaron Lun

Rendered from userguide.Rmd in scrapper 1.1.4.
Guide to ggmanh PackageUpdated 2 months ago

John Lee

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gg4wayUpdated 2 months ago

Ben Laufer

Rendered from gg4way.Rmd in gg4way 1.5.0.
FAERS-PharmacovigilanceUpdated 2 months ago

Yun Peng

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Low Dimensional Projection of Cytometry SamplesUpdated 2 months ago

Philippe Hauchamps, Laurent Gatto

Rendered from CytoMDS.Rmd in CytoMDS 1.3.2.
PiratUpdated 2 months ago

Lucas Etourneau, Samuel Wieczorek"

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MSstatsPTM LabelFree WorkflowUpdated 2 months ago

Devon Kohler ([email protected])

Rendered from MSstatsPTM_LabelFree_Workflow.Rmd in MSstatsPTM 2.9.0.
Making comparisons for differential abundance using contrastsUpdated 2 months ago

Mike Morgan

Rendered from milo_contrasts.Rmd in miloR 2.3.0.
scDotPlotUpdated 2 months ago

Ben Laufer

Rendered from scDotPlot.Rmd in scDotPlot 1.1.0.
PoDCall: Positive Droplet Caller for DNA Methylation ddPCRUpdated 2 months ago

Hans Petter Brodal

Rendered from PoDCall.Rmd in PoDCall 1.15.0.
Example UsageUpdated 2 months ago

Jonathan Carroll

Rendered from example_usage.Rmd in DFplyr 1.1.0.
Saving and reloading DelayedArray objectsUpdated 2 months ago

Aaron Lun

Rendered from userguide.Rmd in chihaya 1.7.0.
The mpra User's GuideUpdated 2 months ago

Leslie Myint, Kasper Daniel Hansen

Rendered from mpra.Rmd in mpra 1.29.0.
Using R client for KoinaUpdated 2 months ago

Ludwig Lautenbacher, Christian Panse

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The mosdef User's GuideUpdated 2 months ago

Leon Dammer, Federico Marini

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ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataUpdated 2 months ago

Etienne A. Thevenot

Rendered from ropls-vignette.Rmd in ropls 1.39.0.
The simplifyEnrichment packageUpdated 2 months ago

Zuguang Gu ([email protected])

Rendered from simplifyEnrichment.Rmd in simplifyEnrichment 2.1.0.
spatialSimGP TutorialUpdated 2 months ago

Kinnary H. Shah, Boyi Guo, Stephanie C. Hicks

Rendered from spatialSimGP.Rmd in spatialSimGP 1.1.0.
GeneNetworkBuilder GuideUpdated 2 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from GeneNetworkBuilder_vignettes.Rmd in GeneNetworkBuilder 1.49.0.
Generate Network from a list of geneUpdated 2 months ago

Jianhong Ou

Rendered from GeneNetworkFromGenes.Rmd in GeneNetworkBuilder 1.49.0.
Introduction_2_loadvariantsUpdated 2 months ago

Hangjia Zhao

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Introduction to DNABarcodeCompatibilityUpdated 2 months ago

Céline Trébeau, Jacques Boutet de Monvel, Fabienne Wong Jun Tai, Raphaël Etournay

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The HilbertCurve packageUpdated 2 months ago

Zuguang Gu ([email protected])

Rendered from HilbertCurve.Rmd in HilbertCurve 2.1.0.
Data visualization with epiregulon.extraUpdated 3 months ago

Xiaosai Yao, Tomasz Włodarczyk

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methyLImp2 vignetteUpdated 3 months ago

Anna Plaksienko

Rendered from methyLImp2_vignette.Rmd in methyLImp2 1.3.0.
CatsCradle Example DataUpdated 3 months ago

Anna Laddach and Michael Shapiro

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CatsCradle Quick StartUpdated 3 months ago

Anna Laddach and Michael Shapiro

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CatsCradle SingleCellExperiment Quick StartUpdated 3 months ago

Anna Laddach and Michael Shapiro

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CatsCradle Spatial VignetteUpdated 3 months ago

Anna Laddach and Michael Shapiro

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Cardinal 3: Statistical methods for mass spectrometry imagingUpdated 3 months ago

Kylie Ariel Bemis

Rendered from Cardinal3-stats.Rmd in Cardinal 3.9.0.
Reading Zarr arrays with RarrUpdated 3 months ago

Mike L. Smith

Rendered from Rarr.Rmd in Rarr 1.7.0.
Detecting differentially abundant subpopulations in mass cytometry dataUpdated 3 months ago

Aaron Lun

Rendered from cydar.Rmd in cydar 1.31.0.
trackViewer Vignette: lollipopPlotUpdated 3 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from lollipopPlot.Rmd in trackViewer 1.43.1.
Introduction to the tidysbml packageUpdated 3 months ago

Veronica Paparozzi

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The iSEEhex packageUpdated 3 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from iSEEhex.Rmd in iSEEhex 1.9.0.
A quick introduction to the updateObject packageUpdated 3 months ago

Hervé Pagès

Rendered from updateObject.Rmd in updateObject 1.11.0.
Getting Started Updated 3 months ago

Hechen Li

Rendered from workflow.Rmd in scMultiSim 1.3.0.
Simulating Multimodal Single-cell Datasets Updated 3 months ago

Hechen Li

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Parameter Guide Updated 3 months ago

Hechen Li

Rendered from options.Rmd in scMultiSim 1.3.0.
GRaNIE single-cell eGRN inferenceUpdated 3 months ago

Christian Arnold

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Pathway AnalysisUpdated 3 months ago

by Alexander Pico

Rendered from Pathway-Analysis.Rmd in rWikiPathways 1.27.0.
systemPipeR: Workflow Environment for Data Analysis and Report GenerationUpdated 3 months ago

Author: Le Zhang, Daniela Cassol, and Thomas Girke

Rendered from systemPipeR.Rmd in systemPipeR 2.13.0.
Analysis of MCIA DecompositionUpdated 3 months ago

Max Mattessich, Joaquin Reyna, Edel Aron, Anna Konstorum

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Predicting New MCIA scoresUpdated 3 months ago

Max Mattessich, Joaquin Reyna, Edel Aron, Anna Konstorum

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Single Cell AnalysisUpdated 3 months ago

Max Mattessich, Joaquin Reyna, Edel Aron, Anna Konstorum

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The database manager in OmnipathRUpdated 3 months ago

Denes Turei

Rendered from db_manager.Rmd in OmnipathR 3.15.0.
OmniPath Bioconductor workshopUpdated 3 months ago

Denes Turei, Alberto Valdeolivas, Attila Gabor, Julio Saez-Rodriguez

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Using escape to perform gene set enrichment analyses on single-cell RNA-seq dataUpdated 3 months ago

Nick Borcherding, Jared Andrews

Rendered from vignette.Rmd in escape 2.3.0.
GETTING STARTED with tidytofUpdated 3 months ago

Timothy Keyes

Rendered from tidytof.Rmd in tidytof 1.1.0.
Reading and writing dataUpdated 3 months ago

Timothy Keyes

Rendered from reading-and-writing-data.Rmd in tidytof 1.1.0.
Quality controlUpdated 3 months ago

Timothy Keyes

Rendered from quality-control.Rmd in tidytof 1.1.0.
PreprocessingUpdated 3 months ago

Timothy Keyes

Rendered from preprocessing.Rmd in tidytof 1.1.0.
DownsamplingUpdated 3 months ago

Timothy Keyes

Rendered from downsampling.Rmd in tidytof 1.1.0.
Dimensionality reductionUpdated 3 months ago

Timothy Keyes

Rendered from dimensionality-reduction.Rmd in tidytof 1.1.0.
Clustering and metaclusteringUpdated 3 months ago

Timothy Keyes

Rendered from clustering.Rmd in tidytof 1.1.0.
Differential discovery analysisUpdated 3 months ago

Timothy Keyes

Rendered from differential-discovery-analysis.Rmd in tidytof 1.1.0.
Feature extractionUpdated 3 months ago

Timothy Keyes

Rendered from feature-extraction.Rmd in tidytof 1.1.0.
Building predictive modelsUpdated 3 months ago

Timothy Keyes

Rendered from modeling.Rmd in tidytof 1.1.0.
How to contribute codeUpdated 3 months ago

Timothy Keyes

Rendered from contributing-to-tidytof.Rmd in tidytof 1.1.0.
Identification and analysis of miRNA sponge regulationUpdated 3 months ago

Junpeng Zhang ([email protected]) School of Engineering, Dali University

Rendered from miRspongeR.Rmd in miRspongeR 2.11.0.
miRBaseConverter: A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versionsUpdated 3 months ago

Taosheng Xu

Rendered from miRBaseConverter-vignette.Rmd in miRBaseConverter 1.31.0.
Improving NCBI GEO submissions of scRNA-seq dataUpdated 3 months ago

Rui Fu

Rendered from geo-annotations.Rmd in clustifyr 1.19.0.
Introduction to clustifyrUpdated 3 months ago

Rui Fu, Austin Gillen, Ryan Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay Hesselberth, Kent Riemondy

Rendered from clustifyr.Rmd in clustifyr 1.19.0.
Analyzing High Density Peptide Array Data using HERONUpdated 3 months ago

Sean McIlwain

Rendered from full_analysis.Rmd in HERON 1.5.0.
DegCre Introduction and ExamplesUpdated 3 months ago

Brian S. Roberts

Rendered from degcre_introduction_and_examples.Rmd in DegCre 1.3.0.
OmnipathR: an R client for the OmniPath web serviceUpdated 3 months ago

Alberto Valdeolivas, Attila Gabor, Denes Turei, Julio Saez-Rodriguez

Rendered from omnipath_intro.Rmd in OmnipathR 3.15.0.
Building prior knowledge network (PKN) for COSMOSUpdated 3 months ago

Denes Turei

Rendered from cosmos.Rmd in OmnipathR 3.15.0.
DEqMS R Markdown vignettesUpdated 3 months ago

Yafeng Zhu, Lukas Orre, Yan Tran, Georgios Mermelekas, Henrik Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö

Rendered from DEqMS-package-vignette.Rmd in DEqMS 1.25.0.
CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomesUpdated 3 months ago

Jianqiang Sun, Xi Fu, Wei Cao

Rendered from CircSeqAlignTk.Rmd in CircSeqAlignTk 1.9.0.
ADAPT TutorialUpdated 3 months ago

Mukai Wang

Rendered from ADAPT-manual.Rmd in ADAPT 1.1.0.
Querying protein featuresUpdated 3 months ago

Johannes Rainer

Rendered from proteins.Rmd in ensembldb 2.31.0.
Using a MySQL server backendUpdated 3 months ago

Johannes Rainer

Rendered from MySQL-backend.Rmd in ensembldb 2.31.0.
Normalization MethodsUpdated 3 months ago

Pol Castellano-Escuder, Ph.D.

Rendered from POMA-normalization.Rmd in POMA 1.17.5.
Pathway constructionUpdated 3 months ago

Denes Turei

Rendered from paths.Rmd in OmnipathR 3.15.0.
Resource specific interaction attributesUpdated 3 months ago

Denes Turei

Rendered from extra_attrs.Rmd in OmnipathR 3.15.0.
Building protein networks around drug-targets using OmnipathRUpdated 3 months ago

Attila Gabor, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered from drug_targets.Rmd in OmnipathR 3.15.0.
Using NicheNet with OmnipathRUpdated 3 months ago

Denes Turei, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered from nichenet.Rmd in OmnipathR 3.15.0.
rSWeeP: Alignment-free method for vectorising biological sequencesUpdated 3 months ago

Camila Pereira Perico, Danrley Rafael Fernandes, Julia Formighieri Varaschin, Camilla Reginatto De Pierri, Mariane Gonçalves Kulik, Ricardo Assunção Vialle, Roberto Tadeu Raittz

Rendered from rSWeeP.Rmd in rSWeeP 1.19.0.
ChIPpeakAnno: annotate, visualize, and compare peak dataUpdated 3 months ago

Jianhong Ou, Kai Hu, Haibo Liu, Junhui Li, Jun Yu, Lihua Julie Zhu

Rendered from ChIPpeakAnno.Rmd in ChIPpeakAnno 3.41.0.
CaMutQC: Cancer Mutation Quality ControlUpdated 3 months ago

Xin Wang [email protected]

Rendered from CaMutQC-manual.Rmd in CaMutQC 1.3.0.
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacksUpdated 3 months ago

Ghislain FIEVET [email protected]

Rendered from vign01_adverSCarial.Rmd in adverSCarial 1.5.0.
Using scifer to filter single-cell sorted B cell receptor (BCR) sanger sequencesUpdated 3 months ago

Rodrigo Arcoverde Cerveira, Matthew James Hinchcliff

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Counting barcodes in sequencing screensUpdated 4 months ago

Aaron Lun

Rendered from counting.Rmd in screenCounter 1.7.0.
Analyzing cell-free DNA methylation data with cfToolsUpdated 4 months ago

Ran Hu, Mary Louisa Stackpole, Shuo Li, Xianghong Jasmine Zhou, Wenyuan Li

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Assortment of header-only librariesUpdated 4 months ago

Aaron Lun

Rendered from userguide.Rmd in assorthead 1.1.4.
LC-MS/MS data analysis with xcmsUpdated 4 months ago

Steffen Neumann

Rendered from xcms-lcms-ms.Rmd in xcms 4.5.1.
Get Started with dominoSignalUpdated 4 months ago

Jacob T Mitchell

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A Tutorial for PepSetTestUpdated 4 months ago

Junmin Wang

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Annotating LC/MS data with cliqueMSUpdated 4 months ago

Oriol Senan

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ChemmineOB: Interface to a Subset of OpenBabel FunctionalitiesUpdated 4 months ago

Authors: Kevin Horan, Thomas Girke

Rendered from ChemmineOB.Rmd in ChemmineOB 1.45.0.
Using RQT, an R package for gene-level meta-analysisUpdated 4 months ago

Ilya Y. Zhbannikov

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motifbreakR: an IntroductionUpdated 4 months ago

Simon G. Coetzee, Gerhard A. Coetzee and Dennis J. Hazelett

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Generate transcript to gene file for bustoolsUpdated 4 months ago

Lambda Moses

Rendered from tr2g.Rmd in BUSpaRse 1.21.0.
An Introduction to goSorensen R-PackageUpdated 4 months ago

Jordi Ocaña, Pablo Flores

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IsoBayesUpdated 4 months ago

Jordy Bollon, Simone Tiberi

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An Irrelevance Threshold Matrix of Dissimilarities.Updated 4 months ago

Pablo Flores, Jordi Ocaña

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READMEUpdated 4 months ago

Pablo Flores

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automatic RNA-Seq present/absent gene expression calls generationUpdated 4 months ago

Julien Wollbrett, Sara Fonseca Costa, Marc Robinson-Rechavi, Frederic Bastian

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OncoSimulR: forward genetic simulation in asexual populations with arbitrary epistatic interactions and a focus on modeling tumor progression.Updated 4 months ago

Ramon Diaz-Uriarte, Sergio Sanchez-Carrillo, Juan Antonio Miguel-Gonzalez, Javier López Cano, Alberto González Klein, Javier Muñoz Haro Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid, and Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Spain.\ [email protected], [email protected], https://ligarto.org/rdiaz

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systemPipeR: Workflow TemplatesUpdated 4 months ago

Author: Le Zhang, Daniela Cassol, and Thomas Girke

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ompBAM API DocumentationUpdated 4 months ago

Alex C H Wong

Rendered from ompBAM-API-Docs.Rmd in ompBAM 1.11.0.
scMitoMut demo: CRC datasetUpdated 4 months ago

Wenjie Sun

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Freezing Python versions inside Bioconductor packagesUpdated 4 months ago

Aaron Lun

Rendered from motivation.Rmd in basilisk 1.19.0.
Introduction to MicrobiotaProcessUpdated 4 months ago

| Shuangbin Xu and GuangChuang Yu | School of Basic Medical Sciences, Southern Medical University

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Base functions and classes for CRISPR gRNA designUpdated 4 months ago

Jean-Philippe Fortin

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A Vignette for DeMixTUpdated 4 months ago

Ruonan Li

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Using concordex in to assess cluster boundaries in scRNA-seqUpdated 4 months ago

Lambda Moses, Kayla Jackson

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Overview of concordexRUpdated 4 months ago

Lambda Moses, Kayla Jackson

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extraChIPs: Differential Signal Using Sliding WindowsUpdated 4 months ago

Stevie Pederson

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ccImpute Package ManualUpdated 4 months ago

Marcin Malec, Parichit Sharma, Hasan Kurban, Mehmet Dalkilic

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Handling large H5AD datasetsUpdated 4 months ago

Developed by Gabriel Hoffman

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Introduction to SeahtrueUpdated 4 months ago

Vincent C. J. de Boer, Gerwin Smits, Xiang Zhang

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Interacting with domino ObjectsUpdated 4 months ago

Jacob T Mitchell

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Plotting Functions and OptionsUpdated 4 months ago

Jacob T Mitchell

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Matter 2: User guide for flexible out-of-memory data structuresUpdated 4 months ago

Kylie Ariel Bemis

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Matter 2: Signal and image processingUpdated 4 months ago

Kylie Ariel Bemis

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Vign03_adapt_classifiersUpdated 4 months ago

Ghislain FIEVET

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Inferring Immune Interactions in Breast CancerUpdated 4 months ago

Orian Stapleton

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GINA in the GWAS.BAYES PackageUpdated 4 months ago

Jacob Williams, Shuangshuang Xu, and Marco A.R. Ferreira

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OverviewUpdated 4 months ago

William Hutchison, Stefano Mangiola

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Introduction to tidyCoverageUpdated 5 months ago

Jacques Serizay

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Simulating bulk Multi-Omics Data with MOSimUpdated 5 months ago

Carlos Martínez, Carolina Monzó, Sonia Tarazona

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Simulating Single-Cell Multi-Omics Data with MOSimUpdated 5 months ago

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Dreamlet analysis of single cell RNA-seqUpdated 5 months ago

Developed by Gabriel Hoffman

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miaVizUpdated 5 months ago

Tuomas Borman

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Saving SummarizedExperiments to artifacts and back againUpdated 5 months ago

Aaron Lun

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VCF filter rulesUpdated 5 months ago

Kévin Rue-Albrecht

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gDRutilsUpdated 5 months ago

gDR team

Rendered from gDRutils.Rmd in gDRutils 1.5.2.
lute algorithm class definitions and usesUpdated 5 months ago

Sean K. Maden, Stephanie C. Hicks

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The lute user's guideUpdated 5 months ago

Sean K. Maden, Stephanie C. Hicks

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Introduction to AnVILBaseUpdated 5 months ago

Bioconductor AnVIL SIG

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qc-tidyingUpdated 5 months ago

Oliver M. Crook

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SGCP package manualUpdated 5 months ago

Niloofar Aghaieabiane

Rendered from SGCP.Rmd in SGCP 1.7.0.
Introduction to hermesUpdated 5 months ago

Daniel Sabanés Bové, Namrata Bhatia, Stefanie Bienert, Benoit Falquet, Haocheng Li, Jeff Luong, Lyndsee Midori Zhang, Alex Richardson, Simona Rossomanno, Tim Treis, Mark Yan, Naomi Chang, Chendi Liao, Carolyn Zhang, Joseph N. Paulson

Rendered from hermes.Rmd in hermes 1.11.0.
MatrixQCvis: shiny-based interactive data quality exploration of omics dataUpdated 5 months ago

Thomas Naake and Wolfgang Huber

Rendered from MatrixQCvis.Rmd in MatrixQCvis 1.15.0.
A. IntroductionUpdated 5 months ago

Martin Morgan

Rendered from introduction.Rmd in AlphaMissenseR 1.3.0.
C. ClinVar IntegrationUpdated 5 months ago

Martin Morgan

Rendered from clinvar.Rmd in AlphaMissenseR 1.3.0.
Cepo for differential stability analysis of scRNA-seq dataUpdated 5 months ago

Hani Jieun Kim

Rendered from cepo.Rmd in Cepo 1.13.0.
Using a BioMart other than EnsemblUpdated 5 months ago

Steffen Durinck, Wolfgang Huber, Mike Smith

Rendered from accessing_other_marts.Rmd in biomaRt 2.63.0.
Using the ResidualMatrix classUpdated 5 months ago

Aaron Lun

Rendered from ResidualMatrix.Rmd in ResidualMatrix 1.17.0.
Differential discovery with CATALYSTUpdated 5 months ago

Helena L Crowell, Mark D Robinson

Rendered from differential.Rmd in CATALYST 1.31.1.
BioTIP: an R-package for Characterization of Biological Tipping-PointsUpdated 5 months ago

Zhezhen Wang, Andrew Goldstein, Yuxi Sun, Biniam Feleke, Qier An, Antonio Feliciano, Ieva Tolkaciovaite, and Xinan H Yang

Rendered from BioTIP.Rmd in BioTIP 1.21.0.
CoGAPS - Coordinated Gene Association in Pattern SetsUpdated 5 months ago

Jeanette Johnson, Ashley Tsang, Thomas Sherman, Genevieve Stein-O'Brien, Hyejune Limb, Elana Fertig

Rendered from CoGAPS.Rmd in CoGAPS 3.27.0.
Analysis of Bead-level Data using beadarrayUpdated 5 months ago

Mark Dunning

Rendered from beadlevel.Rmd in beadarray 2.57.0.
Image Analysis with beadarrayUpdated 5 months ago

Mike Smith

Rendered from ImageProcessing.Rmd in beadarray 2.57.0.
Evaluation of Bioinformatics Metrics with evaluomeRUpdated 5 months ago

José Antonio Bernabé-Díaz, Manuel Franco, Juana-María Vivo, Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis

Rendered from manual.Rmd in evaluomeR 1.23.0.
Accessing the KEGG REST APIUpdated 5 months ago

Bioconductor Package Maintainer

Rendered from KEGGREST-vignette.Rmd in KEGGREST 1.47.0.
Introduction to SANTAUpdated 5 months ago

Alex Cornish

Rendered from SANTA-vignette.Rmd in SANTA 2.43.0.
Epiregulon tutorial with MultiAssayExperimentUpdated 5 months ago

Xiaosai Yao

Rendered from multiome.mae.Rmd in epiregulon 1.3.0.
A guide to metadata for samples and differential expression analysesUpdated 5 months ago

B. Ogan Mancarci

Rendered from metadata.Rmd in gemma.R 3.3.0.
Gene Set Analysis in R -- the GSAR PackageUpdated 5 months ago

Yasir Rahmatallah

Rendered from GSAR.Rnw in GSAR 1.41.0.
ENmix User's GuideUpdated 5 months ago

Zongli Xu, Liang Niu, Jack Taylor

Rendered from ENmix.Rmd in ENmix 1.43.2.
Statistical testing of quantitative omics dataUpdated 5 months ago

Veit Schwämmle

Rendered from StatisticalTest.Rmd in PolySTest 1.1.0.
statTargetUpdated 5 months ago

Hemi Luan

Rendered from statTarget.Rmd in statTarget 1.37.0.
goseq User's GuideUpdated 6 months ago

Federico Marini

Rendered from goseq.Rnw in goseq 1.59.0.
RI correction extraUpdated 6 months ago

Alvaro Cuadros-Inostroza

Rendered from RICorrection.Rnw in TargetSearch 2.9.1.
The TargetSearch PackageUpdated 6 months ago

Alvaro Cuadros-Inostroza

Rendered from TargetSearch.Rnw in TargetSearch 2.9.1.
An Introduction to the GenomicRanges PackageUpdated 6 months ago

Marc Carlson, Patrick Aboyoun, Hervé Pagès, and Martin Morgan

Rendered from GenomicRangesIntroduction.Rmd in GenomicRanges 1.59.1.
GenomicRanges HOWTOs Updated 6 months ago

Hervé Pagès

Rendered from GenomicRangesHOWTOs.Rnw in GenomicRanges 1.59.1.
Introduction to AlpsNMR (older API)Updated 6 months ago

AlpsNMR authors

Rendered from Vig01b-introduction-to-alpsnmr-old-api.Rmd in AlpsNMR 4.9.0.
Introduction to AlpsNMRUpdated 6 months ago

AlpsNMR authors

Rendered from Vig01-introduction-to-alpsnmr.Rmd in AlpsNMR 4.9.0.
Introduction to squallmsUpdated 6 months ago

William Kumler

Rendered from intro_to_squallms.Rmd in squallms 1.1.0.
MultipleAlignment ObjectsUpdated 6 months ago

Marc Carlson, Beryl Kanali

Rendered from MultipleAlignments.Rmd in Biostrings 2.75.1.
Annotation & AlignmentUpdated 6 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from Annotation_Alignment.Rmd in ORFik 1.27.0.
Data managementUpdated 6 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from ORFikExperiment.Rmd in ORFik 1.27.0.
ORFik OverviewUpdated 6 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from ORFikOverview.Rmd in ORFik 1.27.0.
Using broadSeq to analyze RNA-seq dataUpdated 6 months ago

Rishi Das Roy

Rendered from broadSeq.Rmd in broadSeq 1.1.0.
IntroductionUpdated 6 months ago

Dany Mukesha

Rendered from Introduction.Rmd in BioGA 1.1.0.
Quickstart Guide to ggseqalignUpdated 6 months ago

Simeon Lim Rossmann

Rendered from ggseqalign.Rmd in ggseqalign 1.1.0.
PhyloProfileUpdated 6 months ago

Vinh Tran

Rendered from PhyloProfile-vignette.Rmd in PhyloProfile 1.21.3.
cbaf: an automated, easy-to-use R package for comparing omic data across multiple cancers / a cancer's subgroupsUpdated 6 months ago

Arman Shahrisa

Rendered from cbaf.Rmd in cbaf 1.29.0.
dream analysisUpdated 6 months ago

Developed by Gabriel Hoffman

Rendered from dream.Rmd in variancePartition 1.37.1.
Using immunogenViewer to evaluate and choose antibodiesUpdated 6 months ago

Katharina Waury

Rendered from immunogenViewer_vignette.Rmd in immunogenViewer 1.1.0.
STRINGdb VignetteUpdated 6 months ago

Damian Szklarczyk

Rendered from STRINGdb.Rnw in STRINGdb 2.19.0.
Computing RNA velocity in a Bioconductor frameworkUpdated 6 months ago

Kevin Rue-Albrecht, Aaron Lun, Charlotte Soneson

Rendered from velociraptor.Rmd in velociraptor 1.17.0.
Creating CompoundDb annotation resourcesUpdated 6 months ago

Johannes Rainer

Rendered from create-compounddb.Rmd in CompoundDb 1.11.0.
Usage of Annotation Resources with the CompoundDb PackageUpdated 6 months ago

Johannes Rainer

Rendered from CompoundDb-usage.Rmd in CompoundDb 1.11.0.
CAGEr: an R package for CAGE (Cap Analysis of Gene Expression) data analysis and promoterome miningUpdated 6 months ago

Vanja Haberle, Charles Plessy, Sarvesh Nikumbh

Rendered from CAGEexp.Rmd in CAGEr 2.13.0.
VariantExperiment: A RangedSummarizedExperiment Container for Large-Scale Variant Data with GDS BackendUpdated 6 months ago

Qian Liu

Rendered from VariantExperiment-class.Rmd in VariantExperiment 1.21.0.
GDSArray: Representing GDS files as array-like objectsUpdated 6 months ago

Qian Liu, Hervé Pagès, Martin Morgan

Rendered from GDSArray.Rmd in GDSArray 1.27.0.
gDRimportUpdated 6 months ago

gDR team

Rendered from gDRimport.Rmd in gDRimport 1.5.2.
User's GuideUpdated 6 months ago

Shian Su

Rendered from UsersGuide.Rmd in NanoMethViz 3.3.0.
Segmenting and normalizing multiplexed imaging data with simpleSegUpdated 6 months ago

Alexander Nicholls, Ellis Patrick, Nicolas Canete

Rendered from simpleSeg.Rmd in simpleSeg 1.9.0.
Getting Started DECIPHERingUpdated 6 months ago

Erik Wright

Rendered from DECIPHERing.Rnw in DECIPHER 3.3.0.
Performing meta-analyses of microbiome studies with MMUPHinUpdated 6 months ago

Siyuan Ma

Rendered from MMUPHin.Rmd in MMUPHin 1.21.0.
The PIUMA package - Phenotypes Identification Using Mapper from topological data AnalysisUpdated 6 months ago

Mattia Chiesa, Laura Ballarini, Alessia Gerbasi, Giuseppe Albi, Arianna Dagliati, Luca Piacentini

Rendered from PIUMA_vignette.Rmd in PIUMA 1.3.0.
Questions and answers from over the yearsUpdated 6 months ago

Sean Davis

Rendered from questions-and-answers.Rmd in GenomicDataCommons 1.31.0.
The seqsetvis packageUpdated 6 months ago

Joseph R Boyd

Rendered from seqsetvis_overview.Rmd in seqsetvis 1.27.0.
funOmicsUpdated 6 months ago

Elisa Gómez de Lope

Rendered from funomics_vignette.Rmd in funOmics 1.1.0.
missMethyl: Analysing Illumina HumanMethylation BeadChip DataUpdated 6 months ago

Belinda Phipson and Jovana Maksimovic

Rendered from missMethyl.Rmd in missMethyl 1.41.0.
Use of CAGE resources with CAGErUpdated 7 months ago

Vanja Haberle, Charles Plessy

Rendered from CAGE_Resources.Rmd in CAGEr 2.13.0.
mobileRNA: Investigate the RNA mobilome & population-scale changes.Updated 7 months ago

Katie Jeynes-Cupper, Marco Catoni

Rendered from mobileRNA.Rmd in mobileRNA 1.3.0.
ClusterFoldSimilarity: comparing cell-groups from independent single-cell experimentsUpdated 7 months ago

Óscar González-Velasco

Rendered from ClusterFoldSimilarity.Rmd in ClusterFoldSimilarity 1.3.0.
Working with large arrays in R (slides from July 2017) Updated 7 months ago

Hervé Pagès

Rendered from A-Working_with_large_arrays.Rnw in DelayedArray 0.33.2.
Implementing A DelayedArray BackendUpdated 7 months ago

Hervé Pagès

Rendered from B-Implementing_a_backend.Rmd in DelayedArray 0.33.2.
A DelayedArray / HDF5Array update (slides from April 2021) Updated 7 months ago

Hervé Pagès

Rendered from C-DelayedArray_HDF5Array_update.Rnw in DelayedArray 0.33.2.
The GenomicDataCommons PackageUpdated 7 months ago

Sean Davis & Martin Morgan

Rendered from overview.Rmd in GenomicDataCommons 1.31.0.
Working with simple somatic mutationsUpdated 7 months ago

Sean Davis

Rendered from somatic_mutations.Rmd in GenomicDataCommons 1.31.0.
multiWGCNA: the full workflowUpdated 7 months ago

Dario Tommasini

Rendered from autism_full_workflow.Rmd in multiWGCNA 1.5.0.
Accessing curated gene expression data with gemma.RUpdated 7 months ago

Javier Castillo-Arnemann, Jordan Sicherman, B. Ogan Mancarci

Rendered from gemma.R.Rmd in gemma.R 3.3.0.
tidyFlowCoreUpdated 7 months ago

Timothy Keyes

Rendered from tidyFlowCore.Rmd in tidyFlowCore 1.1.0.
RCyjs: interactive network visualization using cytoscape.jsUpdated 7 months ago

Paul Shannon

Rendered from RCyjs.Rmd in RCyjs 2.29.0.
Differential abundance testing with Milo - Mouse gastrulation exampleUpdated 7 months ago

Emma Dann, Mike Morgan

Rendered from milo_gastrulation.Rmd in miloR 2.3.0.
The Art of Multiple Sequence Alignment in RUpdated 7 months ago

Erik Wright

Rendered from ArtOfAlignmentInR.Rnw in DECIPHER 3.3.0.
scRNA-Seq Population-level Analysis using GloScopeUpdated 7 months ago

Hao Wang, William Torous, Elizabeth Purdom

Rendered from GloScopeTutorial.Rmd in GloScope 1.5.0.
Overview of VoyagerUpdated 7 months ago

Lambda Moses, Lior Pachter

Rendered from overview.Rmd in Voyager 1.9.1.
Annotation of MS-based Metabolomics DataUpdated 7 months ago

Johannes Rainer

Rendered from MetaboAnnotation.Rmd in MetaboAnnotation 1.11.1.
A meta analysis on effects of Parkinson's Disease using Gemma.RUpdated 7 months ago

B. Ogan Mancarci

Rendered from metanalysis.Rmd in gemma.R 3.3.0.
Get started-with GenomAutomorphismUpdated 7 months ago

Robersy Sanchez

Rendered from GenomAutomorphism.Rmd in GenomAutomorphism 1.9.0.
OUTRIDER: OUTlier in RNA-seq fInDERUpdated 7 months ago

Christian Mertes

Rendered from OUTRIDER.Rnw in OUTRIDER 1.25.0.
HicAggR - In depth tutorialUpdated 7 months ago

Nicolas Chanard, David Depierre, Robel A. Tesfaye, Stéphane Schaak & Olivier Cuvier

Rendered from HicAggR.Rmd in HicAggR 1.3.0.
Get started with limpca.Updated 7 months ago

Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette

Rendered from limpca.Rmd in limpca 1.3.0.
Application of limpca on the Trout transcriptomic dataset.Updated 7 months ago

Benaiche Nadia, Bernadette Govaerts

Rendered from Trout.Rmd in limpca 1.3.0.
Application of limpca on the UCH metabolomics dataset.Updated 7 months ago

Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette

Rendered from UCH.Rmd in limpca 1.3.0.
Fast functional enrichmentUpdated 7 months ago

Marek Gierlinski

Rendered from fenr.Rmd in fenr 1.5.0.
BioNAR: Biological Network Analysis in RUpdated 7 months ago

Colin Mclean, Anatoly Sorokin, T. I. Simpson, J. Douglas Armstrong, Oksana Sorokina

Rendered from BioNAR_overview.Rmd in BioNAR 1.9.0.
PrOCoil - A Web Service and an R Package for Predicting the Oligomerization of Coiled-Coil ProteinsUpdated 7 months ago

Ulrich Bodenhofer

Rendered from procoil.Rnw in procoil 2.35.0.
Using SynExtendUpdated 7 months ago

Nicholas Cooley

Rendered from UsingSynExtend.Rmd in SynExtend 1.19.0.
KeBABS - An R Package for Kernel Based Analysis of Biological SequencesUpdated 7 months ago

Ulrich Bodenhofer

Rendered from kebabs.Rnw in kebabs 1.41.0.
The UPDhmm's User GuideUpdated 7 months ago

Marta Sevilla Porras, Carlos Ruiz Arenas

Rendered from UPDhmm.Rmd in UPDhmm 1.3.0.
msa - An R Package for Multiple Sequence AlignmentUpdated 7 months ago

Ulrich Bodenhofer

Rendered from msa.Rnw in msa 1.39.0.
iPAC: identification of Protein Amino acid MutationsUpdated 7 months ago

Gregory Ryslik

Rendered from iPAC.Rnw in iPAC 1.51.0.
kmcut_introUpdated 7 months ago

Igor B. Kuznetsov

Rendered from kmcut_intro.Rmd in kmcut 1.1.0.
An introduction to the atena packageUpdated 7 months ago

Beatriz Calvo-Serra, Robert Castelo

Rendered from atena.Rmd in atena 1.13.0.
ampliCan OverviewUpdated 7 months ago

Kornel Labun & Eivind Valen

Rendered from amplicanOverview.Rmd in amplican 1.29.0.
Genome intervals and read alignments for functional explorationUpdated 7 months ago

J. Toedling

Rendered from girafe.Rnw in girafe 1.59.0.
Disordered Matrices VignetteUpdated 7 months ago

William McFadden

Rendered from disorderedMatrices-vignette.Rmd in idpr 1.17.0.
An Introduction to ShortReadUpdated 7 months ago

Martin Morgan, Rohit Satyam

Rendered from Overview.Rmd in ShortRead 1.65.0.
igvShiny: a wrapper of IGV in the Shiny appsUpdated 7 months ago

Arkadiusz Gladki

Rendered from igvShiny.Rmd in igvShiny 1.3.0.
PODKAT - An R Package for Association Testing Involving Rare and Private VariantsUpdated 7 months ago

Ulrich Bodenhofer

Rendered from podkat.Rnw in podkat 1.39.0.
MAPFX: MAssively Parallel Flow cytometry XplorerUpdated 7 months ago

Hsiao-Chi Liao and Agus Salim

Rendered from MAPFX_Vignette.Rmd in MAPFX 1.3.0.
Biostrings Quick OverviewUpdated 7 months ago

Hervé Pagès

Rendered from BiostringsQuickOverview.Rnw in Biostrings 2.75.1.
Pairwise Sequence AlignmentsUpdated 7 months ago

Hervé Pagès

Rendered from PairwiseAlignments.Rnw in Biostrings 2.75.1.
Summix2Updated 7 months ago

Audrey Hendricks

Rendered from Summix.rmd in Summix 2.13.0.
Using Phantasus applicationUpdated 7 months ago

Alexey Sergushichev

Rendered from phantasus-tutorial.Rmd in phantasus 1.27.0.
Introduction to proteomics data analysisUpdated 7 months ago

Lieven Clement, Oliver M. Crook

Rendered from cptac.Rmd in msqrob2 1.15.0.
An Introduction to zitoolsUpdated 7 months ago

Carlotta Meyring

Rendered from zitools_tutorial.Rmd in zitools 1.1.0.
multistateQTL: Orchestrating multi-state QTL analysis in RUpdated 7 months ago

Christina B Azodi, Davis McCarthy, Amelia Dunstone

Rendered from multiStateQTL.Rmd in multistateQTL 1.3.0.
SCArray -- Large-scale single-cell omics data manipulation with GDS filesUpdated 7 months ago

Dr. Xiuwen Zheng, Genomics Research Center, AbbVie

Rendered from Overview.Rmd in SCArray 1.15.1.
Large-scale single-cell omics data manipulation with GDS filesUpdated 7 months ago

Dr. Xiuwen Zheng (Genomics Research Center, AbbVie)

Rendered from SCArray.Rmd in SCArray 1.15.1.
hicVennDiagram Vignette: overviewUpdated 7 months ago

Jianhong Ou

Rendered from hicVennDiagram.Rmd in hicVennDiagram 1.5.0.
signifinder vignetteUpdated 7 months ago

Stefania Pirrotta, Enrica Calura

Rendered from signifinder.Rmd in signifinder 1.9.0.
IntroductionUpdated 7 months ago

Constantin Ahlmann-Eltze

Rendered from Introduction.Rmd in lemur 1.5.0.
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data ExtensionsUpdated 7 months ago

Authors: Jianhai Zhang and Thomas Girke

Rendered from spatialHeatmap.Rmd in spatialHeatmap 2.13.0.
How To use the clusterGraph and distGraph classesUpdated 7 months ago

Robert Gentleman, Jeff Gentry, Seth Falcon, Paul Villafuerte

Rendered from clusterGraph.Rmd in graph 1.85.0.
How to use the graph packageUpdated 7 months ago

Robert Gentleman, Seth Falcon, Jeff Gentry, Paul Shannon, Aliyu Atiku Mustapha

Rendered from graph.Rmd in graph 1.85.0.
AnnotationHub How-To'sUpdated 7 months ago

Bioconductor Package Maintainer

Rendered from AnnotationHub-HOWTO.Rmd in AnnotationHub 3.15.0.
The UCSC.utils packageUpdated 7 months ago

Hervé Pagès

Rendered from UCSC.utils.Rmd in UCSC.utils 1.3.0.
RBioFormats: an R interface to the Bio-Formats libraryUpdated 7 months ago

Andrzej Oleś

Rendered from RBioFormats.Rmd in RBioFormats 1.7.0.
An introduction to survClust packageUpdated 7 months ago

Arshi Arora Department of Epidemiology and Biostatistics, MSKCC

Rendered from survClust_vignette.Rmd in survClust 1.1.0.
Managing Mass Spectrometry ExperimentsUpdated 7 months ago

Laurent Gatto

Rendered from MsExperiment.Rmd in MsExperiment 1.9.0.
phantasusLite tutorialUpdated 7 months ago

Alexey Sergushichev

Rendered from phantasusLite-tutorial.Rmd in phantasusLite 1.5.0.
miRNA affinity models and the KdModel classUpdated 7 months ago

Pierre-Luc Germain, Michael Soutschek, Fridolin Gross

Rendered from Kdmodels.Rmd in scanMiR 1.13.0.
HDF5 Compression FiltersUpdated 7 months ago

Mike L. Smith

Rendered from rhdf5filters.Rmd in rhdf5filters 1.19.0.
Core Utils for Metabolomics DataUpdated 7 months ago

Johannes Rainer

Rendered from MetaboCoreUtils.Rmd in MetaboCoreUtils 1.15.0.
ggtreeSpace-Getting StartedUpdated 7 months ago

Lin Li, Guangchuang Yu

Rendered from ggtreeSpace.Rmd in ggtreeSpace 1.3.0.
Adding third party plotsUpdated 7 months ago

Samuel Wieczorek, Thomas Burger

Rendered from addingThirdPartyPlots.Rmd in omXplore 1.1.0.
omXplore: a versatile series of Shiny apps to explore 'omics' dataUpdated 7 months ago

Samuel Wieczorek, Thomas Burger

Rendered from omXplore.Rmd in omXplore 1.1.0.
Impute Covariate Data in RNA-sequencing StudiesUpdated 8 months ago

Brennan H Baker

Rendered from Impute_Covariate_Data_in_RNA_sequencing_Studies.Rmd in RNAseqCovarImpute 1.5.0.
Introduction to the NanoStringRCCSet ClassUpdated 8 months ago

David Henderson, Patrick Aboyoun, Nicole Ortogero, Zhi Yang, Jason Reeves, Kara Gorman, Rona Vitancol, Thomas Smith, Yuqi Ren

Rendered from Introduction.Rmd in NanoStringNCTools 1.15.0.
Single Cell Proteomics data processing and analysisUpdated 8 months ago

Laurent Gatto, Christophe Vanderaa

Rendered from scp.Rmd in scp 1.17.0.
Load Single-Cell Proteomics data using readSCPUpdated 8 months ago

Laurent Gatto, Christophe Vanderaa

Rendered from read_scp.Rmd in scp 1.17.0.
Getting started with 'SpotSweeper'Updated 8 months ago

Michael Totty, Boyi Guo, Stephanie Hicks

Rendered from getting_started.Rmd in SpotSweeper 1.3.0.
MultiRNAflow: A R package for analysing RNA-seq raw counts with different time points and several biological conditions.Updated 8 months ago

Rodolphe Loubaton

Rendered from MultiRNAflow_vignette-knitr.Rnw in MultiRNAflow 1.5.0.
Running MultiRNAflow on a RNA-seq raw counts with different time points and several biological conditionsUpdated 8 months ago

Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois, Laurent Vallat

Rendered from Running_analysis_with_MultiRNAflow.Rmd in MultiRNAflow 1.5.0.
Omada, An unsupervised machine learning toolkit for automated sample clustering of gene expression profilesUpdated 8 months ago

Sokratis Kariotis

Rendered from omada-vignette.Rmd in omada 1.9.0.
timeOmicsUpdated 8 months ago

Antoine Bodein, Olivier Chapleur, Kim-Anh Lê Cao, Arnaud Droit

Rendered from vignette.Rmd in timeOmics 1.19.0.
Multi-sample analysis (10x Visium Human DLPFC)Updated 8 months ago

Joseph Lee

Rendered from multi-sample.Rmd in Banksy 1.3.0.
Spatial data integration with Harmony (10x Visium Human DLPFC)Updated 8 months ago

Joseph Lee

Rendered from batch-correction.Rmd in Banksy 1.3.0.
Mass Spectrometry Data on ExperimentHubUpdated 8 months ago

Laurent Gatto

Rendered from MsDataHub.Rmd in MsDataHub 1.7.0.
rBLAST: R Interface for the Basic Local Alignment Search ToolUpdated 8 months ago

Michael Hahsler and Anurag Nagar

Rendered from blast.Rmd in rBLAST 1.3.0.
A quick overview of the S4Arrays packageUpdated 8 months ago

Hervé Pagès

Rendered from S4Arrays_quick_overview.Rmd in S4Arrays 1.7.1.
A quick introduction to the BSgenomeForge packageUpdated 8 months ago

Atuhurira Kirabo Kakopo, Hervé Pagès

Rendered from QuickBSgenomeForge.Rmd in BSgenomeForge 1.7.0.
Advanced usage of scpUpdated 8 months ago

Laurent Gatto, Christophe Vanderaa

Rendered from advanced.Rmd in scp 1.17.0.
QFeatures in a nutshellUpdated 8 months ago

Laurent Gatto, Christophe Vanderaa

Rendered from QFeatures_nutshell.Rmd in scp 1.17.0.
Reporting missing values for Single Cell ProteomicsUpdated 8 months ago

Christophe Vanderaa, Laurent Gatto

Rendered from reporting_missing_values.Rmd in scp 1.17.0.
Frequently Asked QuestionsUpdated 8 months ago

Xinlin Gao

Rendered from FAQ_assistance.Rmd in TSAR 1.5.0.
TSAR Package StructureUpdated 8 months ago

Xinlin Gao

Rendered from TSAR_Package_Structure.Rmd in TSAR 1.5.0.
TSAR Workflow by CommandUpdated 8 months ago

Xinlin Gao

Rendered from TSAR_Workflow_by_Command.Rmd in TSAR 1.5.0.
TSAR Workflow by ShinyUpdated 8 months ago

Xinlin Gao

Rendered from TSAR_Workflow_by_Shiny.Rmd in TSAR 1.5.0.
RNAdecay Vignette: Normalization, Modeling, and Visualization of RNA Decay DataUpdated 8 months ago

Reed Sorenson | [email protected] | Department of Biology | University of Utah

Rendered from RNAdecay_workflow.Rmd in RNAdecay 1.27.0.
Quantitative features for mass spectrometry dataUpdated 8 months ago

Laurent Gatto

Rendered from QFeatures.Rmd in QFeatures 1.17.0.
User Manual: IgGeneUsageUpdated 8 months ago

SK

Rendered from User_Manual.Rmd in IgGeneUsage 1.21.0.
Creating a Variant-Modified ReferenceUpdated 8 months ago

Stevie Pederson

Rendered from creating_a_new_reference.Rmd in transmogR 1.3.0.
miRSM: inferring miRNA sponge modules in heterogeneous dataUpdated 8 months ago

Junpeng Zhang ([email protected]) School of Engineering, Dali University

Rendered from miRSM.Rmd in miRSM 2.3.0.
An Overview of the S4Vectors packageUpdated 8 months ago

Patrick Aboyoun, Michael Lawrence, Hervé Pagès

Rendered from S4VectorsOverview.Rmd in S4Vectors 0.45.2.
Making TxDb ObjectsUpdated 8 months ago

Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan

Rendered from txdbmaker.Rmd in txdbmaker 1.3.1.
Data visualization from a QFeatures objectUpdated 8 months ago

Laurent Gatto

Rendered from Visualization.Rmd in QFeatures 1.17.0.
Processing quantitative proteomics data with QFeaturesUpdated 8 months ago

Laurent Gatto

Rendered from Processing.Rmd in QFeatures 1.17.0.
Controlling the iSEE interface using speech recognitionUpdated 8 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from voice.Rmd in iSEE 2.19.0.
gINTomics vignetteUpdated 8 months ago

Angelo Velle, Francesco Patanè, Chiara Romualdi

Rendered from gINTomics.Rmd in gINTomics 1.3.0.
LC-MS data preprocessing and analysis with xcmsUpdated 8 months ago

Steffen Neumann

Rendered from xcms.Rmd in xcms 4.5.1.
MsBackendMspUpdated 8 months ago

Johannes Rainer

Rendered from MsBackendMsp.Rmd in MsBackendMsp 1.11.0.
An introduction to the MoleculeExperiment ClassUpdated 8 months ago

Bárbara Zita Peters Couto, Nick Robertson, Mu-Wei Chung, Ellis Patrick, Shila Ghazanfar

Rendered from MoleculeExperiment.Rmd in MoleculeExperiment 1.7.0.
MSstatsBig WorkflowUpdated 8 months ago

Devon Kohler ([email protected])

Rendered from MSstatsBig_Workflow.Rmd in MSstatsBig 1.5.0.
BREW3R.rUpdated 8 months ago

Lucille Lopez-Delisle

Rendered from BREW3R.r.Rmd in BREW3R.r 1.3.0.
Interacting with the gypsum REST APIUpdated 8 months ago

Aaron Lun

Rendered from userguide.Rmd in gypsum 1.3.0.
An introduction to the GenomicScores packageUpdated 8 months ago

Pau Puigdevall, Robert Castelo

Rendered from GenomicScores.Rmd in GenomicScores 2.19.0.
Preprocessing with CATALYSTUpdated 8 months ago

Helena L Crowell, Vito RT Zanotelli, Stéphane Chevrier, Bernd Bodenmiller, Mark D Robinson

Rendered from preprocessing.Rmd in CATALYST 1.31.1.
How to forge a BSgenome data packageUpdated 8 months ago

Hervé Pagès

Rendered from BSgenomeForge.Rnw in BSgenome 1.75.0.
Advanced BSgenomeForge usageUpdated 8 months ago

Hervé Pagès

Rendered from AdvancedBSgenomeForge.Rnw in BSgenomeForge 1.7.0.
A quick start guide to smartid: Scoring and MARker selection method based on modified Tf-IDfUpdated 8 months ago

Jinjin Chen

Rendered from smartid_Demo.Rmd in smartid 1.3.2.
Coercion of GeoMxSet to Seurat and SpatialExperiment ObjectsUpdated 8 months ago

Maddy Griswold

Rendered from GeomxSet_coercions.Rmd in GeomxTools 3.11.0.
Using SQL-backed DataFramesUpdated 8 months ago

Qian Liu, Aaron Lun, Martin Morgan

Rendered from SQLDataFrame_userguide.Rmd in SQLDataFrame 1.21.0.
rRDP: Interface to the RDP ClassifierUpdated 8 months ago

Michael Hahsler and Anurag Nagar

Rendered from rRDP.Rmd in rRDP 1.41.0.
Storing Mass Spectrometry Data in SQL DatabasesUpdated 8 months ago

Johannes Rainer

Rendered from MsBackendSql.Rmd in MsBackendSql 1.7.1.
knowYourCGUpdated 8 months ago

Goldberg David

Rendered from KYCG.Rmd in knowYourCG 1.3.0.
edge PackageUpdated 8 months ago

John D. Storey

Rendered from edge.Rnw in edge 2.39.0.
SPLINTERUpdated 8 months ago

Diana Low

Rendered from vignette.Rmd in SPLINTER 1.33.0.
cTRAP: identifying candidate causal perturbations from differential gene expression dataUpdated 8 months ago

Bernardo P. de Almeida & Nuno Saraiva-Agostinho

Rendered from cTRAP.Rmd in cTRAP 1.25.0.
RNAmodR: analyzing high throughput sequencing data for post-transcriptional RNA modification footprintsUpdated 8 months ago

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered from RNAmodR.Rmd in RNAmodR 1.21.0.
Universe of iSEE panelsUpdated 8 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from iSEEu.Rmd in iSEEu 1.19.0.
The simona packageUpdated 8 months ago

Zuguang Gu ([email protected])

Rendered from simona.Rmd in simona 1.5.0.
Pathview: pathway based data integration and visualizationUpdated 8 months ago

Weijun Luo

Rendered from pathview.Rnw in pathview 1.47.0.
Working with aligned nucleotides (WORK-IN-PROGRESS!)Updated 8 months ago

Hervé Pagès, Halimat C. Atanda

Rendered from WorkingWithAlignedNucleotides.Rmd in GenomicAlignments 1.43.0.
Main vignette: Aberrant expression and splicing analysisUpdated 8 months ago

Alexandre Segers, Jeroen Gilis, Mattias Van Heetvelde, Elfride De Baere, Lieven Clement

Rendered from saseR-vignette.Rmd in saseR 1.3.0.
bettrUpdated 8 months ago

Charlotte Soneson & Federico Marini

Rendered from bettr.Rmd in bettr 1.3.0.
alevinQCUpdated 8 months ago

Charlotte Soneson

Rendered from alevinqc.Rmd in alevinQC 1.23.0.
EpiTxDb: creating an EpiTxDb objectUpdated 8 months ago

Felix G.M. Ernst

Rendered from EpiTxDb-creation.Rmd in EpiTxDb 1.19.0.
The gDNAx packageUpdated 8 months ago

Beatriz Calvo-Serra, Robert Castelo

Rendered from gDNAx.Rmd in gDNAx 1.5.0.
Pairwise Sequence AlignmentsUpdated 8 months ago

Hervé Pagès

Rendered from PairwiseAlignments.Rnw in pwalign 1.3.0.
Extending MetMashRUpdated 8 months ago

Gavin Rhys Lloyd

Rendered from Extending_MetMashR.Rmd in MetMashR 1.1.0.
Training basic model classifying a cell type from scRNA-seq dataUpdated 8 months ago

Vy Nguyen

Rendered from training-basic-model.Rmd in scAnnotatR 1.13.0.
Training model classifying a cell subtype from scRNA-seq dataUpdated 8 months ago

Vy Nguyen

Rendered from training-child-model.Rmd in scAnnotatR 1.13.0.
ginmappeRUpdated 8 months ago

Fernando Sola, Daniel Ayala, Marina Pulido, Rafael Ayala, Lorena López-Cerero, Inma Hernández, David Ruiz

Rendered from ginmappeR.Rmd in ginmappeR 1.3.1.
Inference and Analysis of Synteny NetworksUpdated 8 months ago

Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, Yves Van de Peer

Rendered from syntenet.Rmd in syntenet 1.9.0.
Pseudobulk cell size rescaling exampleUpdated 8 months ago

Sean K. Maden

Rendered from lute_pseudobulk_example.Rmd in lute 1.3.0.
Introduction to txcutrUpdated 8 months ago

Mervin M Fansler

Rendered from intro.Rmd in txcutr 1.13.0.
findIPs: Detect Influential Points for Feature RankingsUpdated 8 months ago

Shuo Wang, Junyan Lu

Rendered from findIPs.Rmd in findIPs 1.3.1.
Inferring differential exon usage in RNA-Seq data with the DEXSeq packageUpdated 8 months ago

Alejandro Reyes, Simon Anders, Wolfgang Huber

Rendered from DEXSeq.Rmd in DEXSeq 1.53.0.
GUIDEseq VignetteUpdated 8 months ago

Lihua Julie Zhu

Rendered from GUIDEseq.Rnw in GUIDEseq 1.37.0.
Tximeta: transcript quantification import with automatic metadataUpdated 8 months ago

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro

Rendered from tximeta.Rmd in tximeta 1.25.0.
spillR VignetteUpdated 8 months ago

Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald, Christof Seiler

Rendered from spillR-vignette.Rmd in spillR 1.3.0.
simPIC: simulating single-cell ATAC-seq dataUpdated 8 months ago

Sagrika Chugh

Rendered from vignette.Rmd in simPIC 1.3.0.
ggspavis overviewUpdated 8 months ago

Lukas M. Weber, Helena L. Crowell, Yixing E. Dong

Rendered from ggspavis_overview.Rmd in ggspavis 1.13.0.
scRNAseqApp GuideUpdated 8 months ago

Jianhong Ou

Rendered from scRNAseqApp.Rmd in scRNAseqApp 1.7.6.
Converting PharmacoSet Drug Response Data into gDR objectUpdated 8 months ago

Jermiah Joseph, Bartosz Czech

Rendered from ConvertingPharmacoSetToGDR.Rmd in gDRimport 1.5.2.
Sequence manipulation and scanningUpdated 8 months ago

Benjamin Jean-Marie Tremblay^[[email protected]]

Rendered from SequenceSearches.Rmd in universalmotif 1.25.1.
Using eisaR for Exon-Intron Split Analysis (EISA)Updated 8 months ago

Michael Stadler

Rendered from eisaR.Rmd in eisaR 1.19.0.
An introduction to QuasRUpdated 9 months ago

Michael Stadler, Dimos Gaidatzis, Charlotte Soneson, Anita Lerch

Rendered from QuasR.Rmd in QuasR 1.47.0.
How to run CaDrA within a Docker EnvironmentUpdated 9 months ago

Reina Chau

Rendered from docker.Rmd in CaDrA 1.5.0.
Permutation-Based TestingUpdated 9 months ago

Reina Chau

Rendered from permutation_based_testing.Rmd in CaDrA 1.5.0.
Introducing the raer packageUpdated 9 months ago

Kent Riemondy, Kristen Wells-Wrasman, Jay Hesselberth

Rendered from raer.Rmd in raer 1.5.0.
MSA2dist VignetteUpdated 9 months ago

Kristian K Ullrich

Rendered from MSA2dist.Rmd in MSA2dist 1.11.1.
Grouping FTICR-MS data with xcmsUpdated 9 months ago

Joachim Bargsten, Johannes Rainer

Rendered from xcms-direct-injection.Rmd in xcms 4.5.1.
Compounding (grouping) of LC-MS featuresUpdated 9 months ago

Steffen Neumann

Rendered from LC-MS-feature-grouping.Rmd in xcms 4.5.1.
gDRcoreUpdated 9 months ago

gDR team

Rendered from gDRcore.Rmd in gDRcore 1.5.2.
Large-scale data handling and processing with SpectraUpdated 9 months ago

RforMassSpectrometry Package Maintainer

Rendered from Spectra-large-scale.Rmd in Spectra 1.17.1.
metagenomeSeq: statistical analysis for sparse high-throughput sequencingUpdated 9 months ago

Joseph N. Paulson

Rendered from metagenomeSeq.Rnw in metagenomeSeq 1.49.0.
MEIGOR: a software suite based on metaheuristics for global optimization in systems biology and bioinformaticsUpdated 9 months ago

Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro F. Villaverde, Julio R. Banga, Julio Saez-Rodriguez

Rendered from MEIGOR-vignette.Rmd in MEIGOR 1.41.0.
Obtaining and Utilizing TxDb ObjectsUpdated 9 months ago

Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan

Rendered from GenomicFeatures.Rmd in GenomicFeatures 1.59.1.
A workflow to study mechanistic indicators for driver gene prediction with MoonlightUpdated 9 months ago

Mona Nourbakhsh^+^ , Astrid Saksager^+^, Nikola Tom, Xi Steven Chen, Antonio Colaprico, Catharina Olsen, Matteo Tiberti, Elena Papaleo

Rendered from Moonlight2R.Rmd in Moonlight2R 1.5.0.
Finding optimal resolution of hierarchical hypotheses with treeclimbRUpdated 9 months ago

Charlotte Soneson and Ruizhu Huang

Rendered from treeclimbR.Rmd in treeclimbR 1.3.0.
Saving objects to artifacts and back againUpdated 9 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.base 1.7.2.
Parameter selection (VeraFISH Mouse Hippocampus)Updated 9 months ago

Joseph Lee

Rendered from parameter-selection.Rmd in Banksy 1.3.0.
MICSQTL: Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait LociUpdated 9 months ago

Yue Pan, Qian Li

Rendered from MICSQTL.Rmd in MICSQTL 1.5.0.
Introduction to SCONEUpdated 9 months ago

Michael Cole and Davide Risso

Rendered from sconeTutorial.Rmd in scone 1.31.0.
An introduction to ZINB-WaVEUpdated 9 months ago

Davide Risso

Rendered from intro.Rmd in zinbwave 1.29.0.
Building a simple annotation databaseUpdated 9 months ago

Panagiotis Moulos

Rendered from sitadela.Rmd in sitadela 1.15.0.
Building an annotation database for metaseqR2Updated 9 months ago

Panagiotis Moulos

Rendered from metaseqr2-annotation.Rmd in metaseqR2 1.19.0.
Gene Ontology Enrichment AnalysisUpdated 9 months ago

Kellen Cresswell, Mikhail Dozmorov

Rendered from Ontology_Analysis.Rmd in TADCompare 1.17.0.
Introduction to M3DropUpdated 9 months ago

Tallulah Andrews

Rendered from M3Drop_Vignette.Rnw in M3Drop 1.33.0.
dinoR-vignetteUpdated 9 months ago

Michaela Schwaiger

Rendered from dinoR-vignette.Rmd in dinoR 1.3.0.
Utilities for multi-modal single-cell analysesUpdated 9 months ago

Aaron Lun

Rendered from overview.Rmd in mumosa 1.15.0.
Other single-cell RNA-seq analysis utilitiesUpdated 9 months ago

Aaron Lun

Rendered from misc.Rmd in scuttle 1.17.0.
Motif import, export, and manipulationUpdated 9 months ago

Benjamin Jean-Marie Tremblay^[[email protected]]

Rendered from MotifManipulation.Rmd in universalmotif 1.25.1.
Introduction to customProDBUpdated 9 months ago

Xiaojing Wang

Rendered from customProDB.Rnw in customProDB 1.47.0.
Spatial Transcriptomics Deconvolution with SPOTlightUpdated 9 months ago

Marc Elosua-Bayes, Helena L. Crowell

Rendered from SPOTlight_kidney.Rmd in SPOTlight 1.11.0.
Starting work with scRepertoire.Updated 9 months ago

Nick Borcherding

Rendered from vignette.Rmd in scRepertoire 2.3.0.
Motif enrichment in genomic regionsUpdated 9 months ago

Gert Hulselmans

Rendered from Tutorial_AnalysisOfGenomicRegions.Rmd in RcisTarget 1.27.0.
Interactive exploration of design matrices with ExploreModelMatrixUpdated 9 months ago

Charlotte Soneson, Federico Marini, Michael I Love, Florian Geier and Michael B Stadler

Rendered from ExploreModelMatrix.Rmd in ExploreModelMatrix 1.19.0.
GrafGen: Classifying Subpopulations of H. pylori GenomesUpdated 9 months ago

William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin and Charles Rabkin

Rendered from vignette.Rmd in GrafGen 1.3.0.
Introduction to tpSVGUpdated 9 months ago

Boyi Guo

Rendered from intro_to_tpSVG.Rmd in tpSVG 1.3.0.
Using gDRstyleUpdated 9 months ago

gDR team

Rendered from gDRstyle.Rmd in gDRstyle 1.5.1.
The rGREAT packageUpdated 9 months ago

Zuguang Gu ([email protected])

Rendered from rGREAT.Rmd in rGREAT 2.9.0.
Training Signalling Pathway Maps to Biochemical Data with Logic-Based Ordinary Differential EquationsUpdated 9 months ago

David Henriques, Thomas Cokelaer, Enio Gjerga, Attila Gabor

Rendered from CNORode-vignette.Rmd in CNORode 1.49.0.
A parser for raw and identification mass-spectrometry dataUpdated 9 months ago

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

Rendered from mzR.Rmd in mzR 2.41.1.
TEKRABberUpdated 9 months ago

Yao-Chung Chen, Katja Nowick

Rendered from TEKRABber.Rmd in TEKRABber 1.11.0.
rhdf5 - HDF5 interface for RUpdated 9 months ago

Bernd Fischer, Mike L. Smith

Rendered from rhdf5.Rmd in rhdf5 2.51.0.
Comparative transcriptomic analysis of hybrids and their progenitorsUpdated 9 months ago

Fabricio Almeida-Silva, Lucas Prost-Boxoen, Yves Van de Peer

Rendered from HybridExpress.Rmd in HybridExpress 1.3.0.
Subsampling single-cell data sets with sketchRUpdated 9 months ago

Charlotte Soneson

Rendered from sketchR.Rmd in sketchR 1.3.0.
projectR VignetteUpdated 9 months ago

Gaurav Sharma, Charles Shin, Jared N. Slosberg, Loyal A. Goff, Genevieve L. Stein-O'Brien

Rendered from projectR.Rmd in projectR 1.23.0.
An introduction to the QTLExperiment classUpdated 9 months ago

Christina B Azodi, Amelia Dunstone, Davis McCarthy

Rendered from QTLExperiment.Rmd in QTLExperiment 1.5.0.
Loading the tidyomics ecosystemUpdated 9 months ago

William Hutchison

Rendered from loading-tidyomics.Rmd in tidyomics 1.3.0.
multiWGCNA: visualizing condition-specific networksUpdated 9 months ago

Dario Tommasini

Rendered from astrocyte_map_v2.Rmd in multiWGCNA 1.5.0.
Converting a gDR-generated MultiAssayExperiment object into a PharmacoSetUpdated 9 months ago

Jermiah Joseph, Bartosz Czech

Rendered from ConvertingMAEtoPharmacoSet.Rmd in gDRimport 1.5.2.
TrajectoryGeometryUpdated 9 months ago

Anna Laddach and Michael Shapiro

Rendered from TrajectoryGeometry.Rmd in TrajectoryGeometry 1.15.0.
Get barcode from 10X Genomics scRNASeq dataUpdated 9 months ago

Wenjie Sun

Rendered from Barcode_in_10X_scRNASeq.Rmd in CellBarcode 1.13.0.
AUCell: Identifying cells with active gene setsUpdated 9 months ago

Gert Hulselmans

Rendered from AUCell.Rmd in AUCell 1.29.0.
trackViewer Vignette: change the track stylesUpdated 9 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from changeTracksStyles.Rmd in trackViewer 1.43.1.
Complex Object (Patient) Clustering with Multi-view Data Using ANFUpdated 9 months ago

Tianle Ma

Rendered from ANF.Rmd in ANF 1.29.0.
a4vignetteUpdated 9 months ago

Laure Cougnaud

Rendered from a4vignette.Rnw in a4 1.55.0.
A quick tour of RCSLUpdated 9 months ago

Qinglin Mei

Rendered from RCSL.Rmd in RCSL 1.15.0.
Overview of katdetectrUpdated 9 months ago

Daan Hazelaar and Job van Riet

Rendered from General_overview.Rmd in katdetectr 1.9.0.
Example for Survival Data -- Breast Invasive CarcinomaUpdated 9 months ago

André Veríssimo

Rendered from example_brca_survival.Rmd in glmSparseNet 1.25.0.
Breast survival dataset using network from STRING DBUpdated 9 months ago

André Veríssimo

Rendered from example_brca_protein-protein-interactions_survival.Rmd in glmSparseNet 1.25.0.
Example for Classification Data -- Breast Invasive CarcinomaUpdated 9 months ago

Marta Lopes and André Veríssimo

Rendered from example_brca_logistic.Rmd in glmSparseNet 1.25.0.
Example for Survival Data -- Prostate AdenocarcinomaUpdated 9 months ago

Marta Lopes and André Veríssimo

Rendered from example_prad_survival.Rmd in glmSparseNet 1.25.0.
Example for Survival Data -- Skin MelanomaUpdated 9 months ago

Eunice Carrasquinha and André Veríssimo

Rendered from example_skcm_survival.Rmd in glmSparseNet 1.25.0.
Separate 2 groups in Cox regressionUpdated 9 months ago

André Veríssimo

Rendered from separate2GroupsCox.Rmd in glmSparseNet 1.25.0.
Informeasure: a tool to quantify nonlinear dependence between variables in biological regulatory networks from an information theory perspectiveUpdated 9 months ago

//\ Chu PAN //\ College of Computer Science and Electronic Engineering, Hunan University

Rendered from Informeasure.Rmd in Informeasure 1.17.0.
Counting reads with summarizeOverlapsUpdated 9 months ago

Hervé Pagès

Rendered from summarizeOverlaps.Rnw in GenomicAlignments 1.43.0.
gDR style guideUpdated 9 months ago

gDR team

Rendered from style_guide.Rmd in gDRstyle 1.5.1.
Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessmentUpdated 10 months ago

Wolfgang Huber, Robert Gentleman

Rendered from matchprobes.Rmd in Biostrings 2.75.1.
Exposome Data Integration with Omic DataUpdated 10 months ago

Carles Hernandez-Ferer and Juan R. Gonzalez

Rendered from exposome_omic_integration.Rmd in omicRexposome 1.29.0.
An R interface to the Ontology Lookup ServiceUpdated 10 months ago

Laurent Gatto

Rendered from rols.Rmd in rols 3.3.0.
Introduction to MCbiclustUpdated 10 months ago

Robert Bentham

Rendered from MCbiclust_vignette.Rmd in MCbiclust 1.31.0.
spatialHeatmap: Co-visualizing Bulk and Single-cell Assay DataUpdated 10 months ago

Authors: Jianhai Zhang and Thomas Girke

Rendered from covisualize.Rmd in spatialHeatmap 2.13.0.
Creating Custom Annotated SVGsUpdated 10 months ago

Authors: Jianhai Zhang

Rendered from custom_SVGs.Rmd in spatialHeatmap 2.13.0.
fastreeR VignetteUpdated 10 months ago

Anestis Gkanogiannis

Rendered from fastreeR_vignette.Rmd in fastreeR 1.11.0.
Protein data using GeomxToolsUpdated 10 months ago

Maddy Griswold

Rendered from Protein_in_GeomxTools.Rmd in GeomxTools 3.11.0.
trackViewer Vignette: overviewUpdated 10 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from trackViewer.Rmd in trackViewer 1.43.1.
Efficient genome searching with Biostrings and the BSgenome data packagesUpdated 10 months ago

Hervé Pagès

Rendered from GenomeSearching.Rnw in BSgenome 1.75.0.
Dealing with Multiple ImputationsUpdated 10 months ago

Carles Hernandez-Ferrer and Juan R. Gonzalez

Rendered from mutiple_imputation_data_analysis.Rmd in rexposome 1.29.0.
Exposome Data AnalysisUpdated 10 months ago

Carles Hernandez-Ferrer, Xavier Escriba-Montagut, Juan R. Gonzalez

Rendered from exposome_data_analysis.Rmd in rexposome 1.29.0.
rhdf5 Practical TipsUpdated 10 months ago

Mike L. Smith

Rendered from practical_tips.Rmd in rhdf5 2.51.0.
ADaCGH2 OverviewUpdated 10 months ago

Ramon Diaz-Uriarte

Rendered from ADaCGH2.Rnw in ADaCGH2 2.47.0.
Molecular subtyping for ovarian cancerUpdated 10 months ago

Gregory M Chen

Rendered from consensusOV.Rmd in consensusOV 1.29.0.
gDR -- data modelUpdated 10 months ago

gDR team

Rendered from gDR-data-model.Rmd in gDRcore 1.5.2.
ggkeggUpdated 10 months ago

Noriaki Sato

Rendered from usage_of_ggkegg.Rmd in ggkegg 1.5.0.
Generating Protein Sequences with Deep Generative ModelsUpdated 10 months ago

Dongmin Jung

Rendered from GenProSeq.Rmd in GenProSeq 1.11.0.
Index file for the qcmetrics package vignetteUpdated 10 months ago

Laurent Gatto

Rendered from qcmetrics.Rmd in qcmetrics 1.45.0.
cBioPortalData: User GuideUpdated 10 months ago

Marcel Ramos & Levi Waldron

Rendered from cBioPortalData.Rmd in cBioPortalData 2.19.1.
MultiAssayExperiment: The Integrative Bioconductor ContainerUpdated 10 months ago

MultiAssay Special Interest Group

Rendered from MultiAssayExperiment.Rmd in MultiAssayExperiment 1.33.1.
RedeR: bridging network analysis and visualizationUpdated 10 months ago

Sysbiolab - Bioinformatics and Systems Biology Laboratory.

Rendered from RedeR.Rmd in RedeR 3.3.0.
Loading and re-analysing public data through ReactomeGSAUpdated 10 months ago

Johannes Griss

Rendered from reanalysing-public-data.Rmd in ReactomeGSA 1.21.0.
Practical uses for provided CpG probe annotationsUpdated 10 months ago

Sean K. Maden

Rendered from cpg_probe_annotations.Rmd in recountmethylation 1.17.0.
A brief introduction to edgeRUpdated 10 months ago

Yunshun Chen

Rendered from intro.Rmd in edgeR 4.5.0.
Comparing totalVI and OSCA book CITE-seq analysesUpdated 10 months ago

OSCA book authors and Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from compch12.Rmd in scviR 1.7.0.
BiocSklearn -- exposing python Scikit machine learning elements for BioconductorUpdated 10 months ago

Vincent J. Carey, stvjc at channing.harvard.edu, Shweta Gopaulakrishnan, reshg at channing.harvard.edu, Samuela Pollack, spollack at jimmy.harvard.edu

Rendered from BiocSklearn.Rmd in BiocSklearn 1.29.0.
ensemblVEP: using the REST API with BioconductorUpdated 10 months ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from ensemblVEP.Rmd in VariantAnnotation 1.53.0.
Error handlingUpdated 10 months ago

Developed by Gabriel Hoffman

Rendered from errors.Rmd in dreamlet 1.5.0.
Using Bioconductor's Annotation LibrariesUpdated 10 months ago

Marc Carlson, Jianhua Zhang, Manvi Yaduvanshi

Rendered from useDataPkgs.Rmd in annotate 1.85.0.
Accessing Ensembl annotation with biomaRtUpdated 10 months ago

Mike L. Smith, Steffen Durinck, Wolfgang Huber

Rendered from accessing_ensembl.Rmd in biomaRt 2.63.0.
The yamss User's GuideUpdated 10 months ago

Leslie Myint, Kasper Daniel Hansen

Rendered from yamss.Rmd in yamss 1.33.0.
DifferentialRegulation: a method to identify genes displaying differential regulation between groups of samplesUpdated 10 months ago

Simone Tiberi, Charlotte Soneson

Rendered from DifferentialRegulation.Rmd in DifferentialRegulation 2.5.0.
Get StartedUpdated 10 months ago

Pol Castellano-Escuder, Ph.D.

Rendered from POMA-workflow.Rmd in POMA 1.17.5.
CellScape vignetteUpdated 10 months ago

Shixiang Wang

Rendered from cellscape_vignette.Rmd in cellscape 1.31.0.
animalculesUpdated 10 months ago

Yue Zhao, Anthony Federico, Evan Johnson

Rendered from animalcules.Rmd in animalcules 1.23.0.
gDR suiteUpdated 10 months ago

gDR team

Rendered from gDR.Rmd in gDR 1.5.1.
Case studiesUpdated 10 months ago

Martin Morgan

Rendered from b_case_studies.Rmd in cellxgenedp 1.11.0.
Discovery and retrievalUpdated 10 months ago

Martin Morgan

Rendered from a_using_cellxgenedp.Rmd in cellxgenedp 1.11.0.
The Magic of Gene FindingUpdated 10 months ago

Erik Wright

Rendered from FindingGenes.Rnw in DECIPHER 3.3.0.
Introduction to biocroxytestUpdated 10 months ago

Francesc Catala-Moll

Rendered from biocroxytest.Rmd in biocroxytest 1.3.0.
flowWorkspace Introduction: A Package to store and maninpulate gated flow dataUpdated 10 months ago

Greg Finak [email protected], Mike Jiang [email protected]

Rendered from flowWorkspace-Introduction.Rmd in flowWorkspace 4.19.0.
How to merge/standardize GatingSetsUpdated 10 months ago

Greg Finak [email protected], Mike Jiang [email protected]

Rendered from HowToMergeGatingSet.Rmd in flowWorkspace 4.19.0.
cgdsr to cBioPortalData: Migration TutorialUpdated 10 months ago

Karim Mezhoud & Marcel Ramos

Rendered from cgdsrMigration.Rmd in cBioPortalData 2.19.1.
Importing from to tRNAdb and mitotRNAdb as GRangesUpdated 11 months ago

Felix G.M. Ernst

Rendered from tRNAdbImport.Rmd in tRNAdbImport 1.25.0.
Large-scale single-cell RNA-seq data analysis using GDS files and SeuratUpdated 11 months ago

Dr. Xiuwen Zheng (Genomics Research Center, AbbVie)

Rendered from SCArray.sat.Rmd in SCArray.sat 1.7.0.
Getting Started with escheRUpdated 11 months ago

Boyi Guo, Stephanie C. Hicks

Rendered from SRT_eg.Rmd in escheR 1.7.0.
Overview of BiocPkgToolsUpdated 11 months ago

Shian Su, Vince Carey, Marcel Ramos, Lori Shepherd, Martin Morgan, Sean Davis

Rendered from BiocPkgTools.Rmd in BiocPkgTools 1.25.2.
Use of SpatialDecon in a small GeoMx datasetUpdated 11 months ago

Maddy Griswold

Rendered from SpatialDecon_vignette.Rmd in SpatialDecon 1.17.0.
Introduction to HiCExperimentUpdated 11 months ago

Jacques Serizay

Rendered from HiCExperiment.Rmd in HiCExperiment 1.7.0.
Description and usage of MsBackendMgfUpdated 11 months ago

RforMassSpectrometry Package Maintainer

Rendered from MsBackendMgf.Rmd in MsBackendMgf 1.15.1.
Filtering and SubsettingUpdated 11 months ago

Francesc Catala-Moll

Rendered from filtering_subsetting.Rmd in dar 1.3.0.
Introduction to darUpdated 11 months ago

Francesc Catala-Moll

Rendered from dar.Rmd in dar 1.3.0.
Workflow with real dataUpdated 11 months ago

Francesc Catala-Moll

Rendered from article.Rmd in dar 1.3.0.
HowTo: Build and use chromosomal informationUpdated 11 months ago

Jeff Gentry, Kritika Verma

Rendered from chromLOC.Rmd in annotate 1.85.0.
GenomicPlot: an R package for efficient and flexible visualization of genome-wide NGS coverage profilesUpdated 11 months ago

Shuye Pu

Rendered from GenomicPlot_vignettes.rmd in GenomicPlot 1.5.0.
Usage of ZygosityPredictorUpdated 11 months ago

Marco Rheinnecker

Rendered from Usage.Rmd in ZygosityPredictor 1.7.0.
SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of InterestUpdated 11 months ago

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Rendered from SummarizedExperiment.Rmd in SummarizedExperiment 1.37.0.
TCCUpdated 11 months ago

Jianqiang Sun

Rendered from TCC.Rnw in TCC 1.47.0.
Domain segmentation (STARmap PLUS mouse brain)Updated 11 months ago

Joseph Lee

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Saving BumpyMatrices to fileUpdated 11 months ago

Aaron Lun

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Saving common bioinformatics file formatsUpdated 11 months ago

Aaron Lun

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Saving XStringSets to artifacts and back againUpdated 11 months ago

Aaron Lun

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Saving MultiAssayExperiments to artifacts and back againUpdated 11 months ago

Aaron Lun

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AnnotationHub: Access the AnnotationHub Web ServiceUpdated 12 months ago

Bioconductor Package Maintainer

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Troubleshoot The HubsUpdated 12 months ago

Lori Shepherd

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"Finding differentially expressed unannotated genomic regions from RNA-seq data with srnadiff"Updated 12 months ago

Matthias Zytnicki, Ignacio González

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SiPSiC - Infer Biological Pathway Activity from Single-Cell RNA-Seq DataUpdated 12 months ago

Daniel Davis

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Biscuiteer User GuideUpdated 12 months ago

Jacob Morrison

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VplotRUpdated 12 months ago

Jacques Serizay

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Reproducibility in Microbiome Data AnalysisUpdated 12 months ago

Francesc Catala-Moll

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treeio: Base Classes and Functions for Phylogenetic Tree Input and OutputUpdated 12 months ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

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Guangchuang Yu and Shuangbin Xu

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Yue Cao

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BERT-VignetteUpdated 12 months ago

Yannis Schumann

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Macarron User ManualUpdated 12 months ago

Amrisha Bhosle, Ludwig Geistlinger, Sagun Maharjan

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RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons.Updated 1 years ago

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Simplifying Genomic Annotations in RUpdated 1 years ago

Mohammed Omar Elsiddieg Abdallah

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betaHMM package: Quick-start guideUpdated 1 years ago

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Pathway activity inference from scRNA-seqUpdated 1 years ago

Pau Badia-i-Mompel

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Pathway activity inference in bulk RNA-seqUpdated 1 years ago

Pau Badia-i-Mompel

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Transcription factor activity inference from scRNA-seqUpdated 1 years ago

Pau Badia-i-Mompel

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Transcription factor activity inference in bulk RNA-seqUpdated 1 years ago

Pau Badia-i-Mompel

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Saving genomic ranges to artifacts and back againUpdated 1 years ago

Aaron Lun

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MACSrUpdated 1 years ago

Qiang Hu

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An overview of topconfectsUpdated 1 years ago

Paul Harrison

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Confident fold changeUpdated 1 years ago

Paul Harrison

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Overview of the tidybulk packageUpdated 1 years ago

Stefano Mangiola

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The Gviz User GuideUpdated 1 years ago

Florian Hahne, Robert Ivánek

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ReUseData: Reusable and Reproducible Data ManagementUpdated 1 years ago

Qian Liu, Qiang Hu, Song Liu, Alan Hutson, Martin Morgan

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ReUseData: Reusable and Reproducible Data Management - quick startUpdated 1 years ago

Qian Liu, Qiang Hu, Song Liu, Alan Hutson, Martin Morgan

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ReUseData: Workflow-based Data Recipes for Management of Reusable and Reproducible Data ResourcesUpdated 1 years ago

Qian Liu

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Beyond Sequence-based Spatially-Resolved DataUpdated 1 years ago

Boyi Guo

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BANDITS: Bayesian ANalysis of DIfferenTial SplicingUpdated 1 years ago

Simone Tiberi

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PLSDA-batch VignetteUpdated 1 years ago

Yiwen (Eva) Wang

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Analysing single-cell RNA-sequencing DataUpdated 1 years ago

Johannes Griss

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Using the ReactomeGSA packageUpdated 1 years ago

Johannes Griss

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Getting Started with ClassifyRUpdated 1 years ago

Dario Strbenac, Ellis Patrick, Graham Mann, Jean Yang, John Ormerod The University of Sydney, Australia.

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Manual for the RCM pacakageUpdated 1 years ago

Stijn Hawinkel

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Differential Expression Meta-Analysis with DExMA packageUpdated 1 years ago

Juan Antonio Villatoro-García

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Getting started with SimBuUpdated 1 years ago

Alexander Dietrich

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Inputs and OutputsUpdated 1 years ago

Alexander Dietrich

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Introducing mRNA bias into simulations with scaling factorsUpdated 1 years ago

Alexander Dietrich

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Public Data Integration using SfairaUpdated 1 years ago

Alexander Dietrich

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DEGseqUpdated 1 years ago

Likun Wang

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TAP-seq primer design workflowUpdated 1 years ago

Andreas Gschwind

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PADOGUpdated 1 years ago

Adi L. Tarca

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The epimutacions User's GuideUpdated 1 years ago

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BICOSS in the GWAS.BAYES PackageUpdated 1 years ago

Jacob Williams and Marco A.R. Ferreira

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Quantifying cell colocalisation with SPIATUpdated 1 years ago

Yuzhou Feng

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sSNAPPY: Singel Sample directioNAl Pathway Perturbation analYsisUpdated 1 years ago

Wenjun Nora Liu, Stephen Pederson

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Motivation and use of RhtslibUpdated 1 years ago

Nathaniel Hayden, Martin Morgan

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Use of SpatialDecon in a large GeoMx dataset with GeomxToolsUpdated 1 years ago

Maddy Griswold

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A quick start guide to the scider packageUpdated 1 years ago

Ning Liu, Mengbo Li, Yunshun Chen

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Modeling continuous cell-level covariatesUpdated 1 years ago

Developed by Gabriel Hoffman

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GRaNIE Workflow ExampleUpdated 1 years ago

Christian Arnold

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Perform Genomic LiftoverUpdated 1 years ago

Abdullah Al Nahid, Hervé Pagès, Michael I. Love

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Accessing Human Cell Atlas DataUpdated 1 years ago

Maya Reed McDaniel

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Working With Human Cell Atlas ManifestsUpdated 1 years ago

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Decontamination of single cell protein expression data with DecontProUpdated 1 years ago

Yuan Yin, Joshua Campbell

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Decontamination of ambient RNA in single-cell genomic data with DecontXUpdated 1 years ago

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4.2 - Schematic plotsUpdated 1 years ago

Tiago Chedraoui Silva

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rtracklayerUpdated 1 years ago

Michael Lawrence

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Linking to Rhdf5libUpdated 1 years ago

Mike L. Smith

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Introduction to crisprShinyUpdated 1 years ago

Luke Hoberecht, Jean-Philippe Fortin

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Reading HDF5 Files In The CloudUpdated 1 years ago

Mike L. Smith

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signeRUpdated 1 years ago

Renan Valieris

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ptairMS: Processing and analysis of PTR-TOF-MS dataUpdated 1 years ago

Camille Roquencourt, Mélanie Bregou, Paul Zheng, Pierrick Roger and Etienne Thevenot

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CRISPRball Quick StartUpdated 1 years ago

Jared Andrews

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scPipe: a flexible data preprocessing pipeline for 3' end scRNA-seq dataUpdated 1 years ago

Luyi Tian

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TCGAutils: Helper functions for working with TCGA datasetsUpdated 1 years ago

Marcel Ramos & Levi Waldron

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An introduction to contrast decomposition and querying using orthosUpdated 1 years ago

Panagiotis Papasaikas, Charlotte Soneson, Michael Stadler

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Using the rrvgo packageUpdated 1 years ago

Sergi Sayols

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Analyzing eCLIP and iCLIP data with DEWSeqUpdated 1 years ago

Sudeep Sahadevan, Thomas Schwarzl

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cBioPortalData: API Reference Guide for DevsUpdated 1 years ago

Marcel Ramos & Levi Waldron

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signeRFlowUpdated 1 years ago

Alexandre Defelicibus

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Using gatom packageUpdated 1 years ago

Anstasiia Gainullina, Mariia Emelianova, Alexey Sergushichev

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GRAPH Interaction from pathway Topological EnvironmentUpdated 1 years ago

Gabriele Sales

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GNOSIS: Genomics explorer using statistical and survival analysis in RUpdated 1 years ago

Lydia King

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circRNAprofiler: An R-based computational framework for the downstream analysis of circular RNAsUpdated 1 years ago

Simona Aufiero

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A framework to discover Spatially Variable genes via spatial clustersUpdated 1 years ago

Peiying Cai, Simone Tiberi

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regionalpcsUpdated 1 years ago

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OverviewUpdated 1 years ago

by Alexander Pico

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Overview of DelayedMatrixStatsUpdated 1 years ago

Peter Hickey

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Customize BioCarta Pathway ImagesUpdated 1 years ago

Zuguang Gu ([email protected])

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GEOexplorerUpdated 1 years ago

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Hi-C arithmetic with plyinteractionsUpdated 1 years ago

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Obtain and Display H3K4Me3 K562 track from UCSC table browserUpdated 1 years ago

Paul Shannon

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plyinteractionsUpdated 1 years ago

Jacques Serizay

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extraChIPs: Differential Signal Using Fixed-Width WindowsUpdated 1 years ago

Stevie Pederson

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PAT-Seq poly(A) tail length example Updated 1 years ago

Paul Harrison

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PAT-Seq alternative polyadenylation example Updated 1 years ago

Paul Harrison

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SLAM-Seq proportion data example Updated 1 years ago

Paul Harrison

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Assessing orthogroup inferenceUpdated 1 years ago

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Usage of the metaseqR2 packageUpdated 1 years ago

Panagiotis Moulos

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Generating visualisations of cell-cell interactions with CCPlotRUpdated 1 years ago

Sarah Ennis, Pilib Ó Broin, Eva Szegezdi

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Modeling the origin of mutations identified in a liquid biopsy: cancer or clonal hematopoiesis?Updated 1 years ago

Adith S. Arun and Robert B. Scharpf

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Classifiers methodsUpdated 1 years ago

Tiago Chedraoui Silva

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ANOVA-Like Differential Expression tool for high throughput sequencing dataUpdated 1 years ago

Greg Gloor

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cytoviewer - Interactive multi-channel image visualization in RUpdated 1 years ago

Lasse Meyer, Nils Eling

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scPipe: a flexible data preprocessing pipeline for scATAC-seq dataUpdated 1 years ago

Shani Amarasinghe, Phil Yang

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BiocBook: write Quarto books with BioconductorUpdated 1 years ago

Jacques Serizay

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Example Data for RNAseqCovarImputeUpdated 1 years ago

Brennan H Baker

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Getting Started with the peakPantheR packageUpdated 1 years ago

Arnaud Wolfer

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Parallel AnnotationUpdated 1 years ago

Arnaud Wolfer

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Real Time AnnotationUpdated 1 years ago

Arnaud Wolfer

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Incorporating Scale Uncertainty into ALDEx2Updated 1 years ago

Michelle Nixon

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Population reference dataset GDS filesUpdated 1 years ago

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

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Attributes for Graph ObjectsUpdated 1 years ago

Seth Falcon, Paul Villafuerte

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The Double Life of RNA: Uncovering Non-Coding RNAsUpdated 1 years ago

Erik Wright

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Visualize Differential Expression resultsUpdated 1 years ago

David Barrios and Carlos Prieto

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Introduction to shiny.gosling Updated 1 years ago

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Using a GRanges object in shiny.gosling Updated 1 years ago

Appsilon

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Creating a Circos Plot with VCF Data Updated 1 years ago

Appsilon

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Creating an Interactive Line Chart with shiny.gosling Updated 1 years ago

Appsilon

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Creating a Multi-Scale Sequence Track Updated 1 years ago

Appsilon

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Example using structToolboxUpdated 1 years ago

Gavin R Lloyd, Ralf J Weber

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Introduction to metabolomicsWorkbenchRUpdated 1 years ago

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Data with outliersUpdated 1 years ago

Henning Redestig

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IntroductionUpdated 1 years ago

Henning Redestig

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sechmUpdated 1 years ago

Pierre-Luc Germain

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A quick start guide to the hoodscanR packageUpdated 1 years ago

Ning Liu, Melissa Davis

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Introduction to iSEEpathwaysUpdated 1 years ago

Kevin Rue-Albrecht

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Overview of the tidySingleCellExperiment packageUpdated 1 years ago

Stefano Mangiola

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The consICa package: User’s manualUpdated 1 years ago

Petr V. Nazarov, Tony Kaoma, Maryna Chepeleva

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scDesign3 QuickstartUpdated 1 years ago

Dongyuan Song, Qingyang Wang

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GladiaTOX: R Package for Processing High Content Screening dataUpdated 1 years ago

Vincenzo Belcastro, Stephane Cano, Florian Martin

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Individual-specific and cell-type-specific deconvolution using ISLETUpdated 1 years ago

Hao Feng, Qian Li, Guanqun Meng

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Overview of the tidySummarizedExperiment packageUpdated 1 years ago

Stefano Mangiola

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Probabilistic Outlier Identification for RNA Sequencing Generalized Linear ModelsUpdated 1 years ago

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TCseq VignetteUpdated 1 years ago

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planetUpdated 1 years ago

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compSPOT-VignetteUpdated 1 years ago

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HiCDOCUpdated 1 years ago

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Error handlingUpdated 1 years ago

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Frequently asked questionsUpdated 1 years ago

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Multivariate testsUpdated 1 years ago

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The wateRmelon User's GuideUpdated 1 years ago

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CytoPipelineGUI : visualization of Flow Cytometry Data Analysis Pipelines run with CytoPipelineUpdated 1 years ago

Philippe Hauchamps, Laurent Gatto

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Demonstration of the CytoPipeline R package suite functionalitiesUpdated 1 years ago

Philippe Hauchamps, Laurent Gatto

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Integration with other panelsUpdated 1 years ago

Kevin Rue-Albrecht

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Working with the Gene OntologyUpdated 1 years ago

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Introduction to snifterUpdated 1 years ago

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01 BiocHail -- GWAS tutorial from hail.isUpdated 1 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

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03 Working with UK Biobank summary statisticsUpdated 1 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

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MsQuality: Calculation of QC metrics from mass spectrometry dataUpdated 1 years ago

Thomas Naake and Johannes Rainer

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Vign02_overView_analysisUpdated 1 years ago

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Vign04_advRandWalkMinChangeUpdated 1 years ago

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Introduction to bootRangesUpdated 1 years ago

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nnSVG TutorialUpdated 1 years ago

Lukas M. Weber, Stephanie C. Hicks

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Gene coexpression network inferenceUpdated 1 years ago

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Gene regulatory network inferenceUpdated 1 years ago

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Network comparison: consensus modules and module preservationUpdated 1 years ago

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Swish: differential expression accounting for inferential uncertaintyUpdated 1 years ago

Michael Love

Rendered from swish.Rmd in fishpond 2.13.0.
Testing non-linear effectsUpdated 1 years ago

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Rendered from non_lin_eff.Rmd in dreamlet 1.5.0.
Variance partitioning analysisUpdated 1 years ago

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Additional visualizations of variance structureUpdated 1 years ago

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Theory and practice of random effectsUpdated 1 years ago

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Guangchuang Yu

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Tutorial of the SARC R Package. Flagging the confidence of CNVs from WES/ WGS cohorts.Updated 1 years ago

by Krutik Patel, PhD

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Introduction to BiocParallel Updated 1 years ago

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mbQTL_VignetteUpdated 1 years ago

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GENIE3 vignetteUpdated 1 years ago

Van Anh Huynh-Thu ([email protected])

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CardinalIO: Parsing and writing imzML filesUpdated 1 years ago

Kylie Ariel Bemis

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mashr analysis after dreamletUpdated 1 years ago

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Working with transcriptsUpdated 1 years ago

Haakon Tjeldnes & Kornel Labun

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Rcwl: An R interface to the Common Workflow Language (CWL)Updated 1 years ago

Qiang Hu, Qian Liu

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Matching case study I: CTCF occupancyUpdated 1 years ago

Eric S. Davis

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Matching case study II: CTCF orientationUpdated 1 years ago

Eric S. Davis

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Report breakdown by groupUpdated 1 years ago

ampliCan

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Report breakdown by guideRNAUpdated 1 years ago

ampliCan

Rendered from example_guide_report.Rmd in amplican 1.29.0.
Summarization and quantitative trait analysis of CNV rangesUpdated 1 years ago

Vinicius Henrique da Silva, Ludwig Geistlinger

Rendered from CNVRanger.Rmd in CNVRanger 1.23.0.
Seamless navigation through combined results of set- & network-based enrichment analysisUpdated 1 years ago

Ludwig Geistlinger

Rendered from EnrichmentBrowser.Rmd in EnrichmentBrowser 2.37.0.
MSstats: Protein/Peptide significance analysisUpdated 1 years ago

Meena Choi

Rendered from MSstats.Rmd in MSstats 4.15.0.
Introduction to singleCellTKUpdated 1 years ago

Yichen Wang, Irzam Sarfraz, Rui Hong, Yusuke Koga, Salam Abdullatif, Nida Pervaiz, David Jenkins, Vidya Akavoor, Xinyun Cao, Shruthi Bandyadka, Anastasia Leshchyk, Tyler Faits, Mohammed Muzamil Khan, Zhe Wang, W. Evan Johnson, Ming Liu, Joshua D. Campbell

Rendered from singleCellTK.Rmd in singleCellTK 2.17.0.
SDAMS VignetteUpdated 1 years ago

Yuntong Li

Rendered from SDAMS.Rnw in SDAMS 1.27.0.
An overview of the epistack packageUpdated 1 years ago

Guillaume Devailly

Rendered from using_epistack.Rmd in epistack 1.13.0.
R packages: CellScoreUpdated 1 years ago

Nancy Mah

Rendered from CellScoreVignette.Rnw in CellScore 1.27.0.
Analyzing Targeted Bisulfite Sequencing data with SOMNiBUSUpdated 1 years ago

Kaiqiong Zhao

Rendered from SOMNiBUS.Rmd in SOMNiBUS 1.13.0.
An R Package for fast segmentationUpdated 1 years ago

Günter Klambauer, Andreas Mitterecker

Rendered from fastseg.Rmd in fastseg 1.53.2.
EpiMixUpdated 1 years ago

| Yuanning Zheng, John Jun, Kevin Brennan and Olivier Gevaert | | Stanford Center for Biomedical Informatics Research (BIMR) | Department of Medicine | 1265 Welch Road | Stanford CA, 94305-5479

Rendered from Methylation_Modeling.Rmd in EpiMix 1.9.0.
Doublet identifiation in single-cell ATAC-seqUpdated 1 years ago

Pierre-Luc Germain

Rendered from scATAC.Rmd in scDblFinder 1.21.0.
Adding a custom header and footer to the landing pageUpdated 1 years ago

Kevin Rue-Albrecht

Rendered from header.Rmd in iSEEindex 1.5.0.
easier User Manual {#id .class width=60 height=60}Updated 1 years ago

Oscar Lapuente-Santana, Federico Marini, Arsenij Ustjanzew, Francesca Finotello, Federica Eduati

Rendered from easier_user_manual.Rmd in easier 1.13.0.
UniProt.ws: A package for retrieving data from the UniProt web serviceUpdated 1 years ago

Marc Carlson

Rendered from UniProt.ws.Rmd in UniProt.ws 2.47.1.
tweeDEseq: analysis of RNA-seq data using the Poisson-Tweedie family of distributionsUpdated 1 years ago

Dolors Pelegri-Siso

Rendered from tweeDEseq.Rnw in tweeDEseq 1.53.0.
SpectralTAD VignetteUpdated 1 years ago

Kellen Cresswell, John Stansfield, Mikhail Dozmorov

Rendered from SpectralTAD.Rmd in SpectralTAD 1.23.0.
Demonstration of the CytoPipeline R package suite functionalitiesUpdated 1 years ago

Philippe Hauchamps, Laurent Gatto

Rendered from Demo.Rmd in CytoPipeline 1.7.0.
R-side access to published microbial signatures from BugSigDBUpdated 1 years ago

Ludwig Geistlinger, Jennifer Wokaty, and Levi Waldron

Rendered from bugsigdbr.Rmd in bugsigdbr 1.13.0.
iNETgrate: Integrating gene expression and DNA methylation data in a gene networkUpdated 1 years ago

Habil Zare

Rendered from iNETgrate_inference.Rnw in iNETgrate 1.5.0.
Advanced baySeq analysesUpdated 1 years ago

Samuel Granjeaud

Rendered from baySeq_generic.Rnw in baySeq 2.41.0.
Introduction to matchRangesUpdated 1 years ago

Eric S. Davis

Rendered from matchRanges.Rmd in nullranges 1.13.0.
Preparing Affymetrix DataUpdated 1 years ago

GENEVA Coordinating Center, Sonali Kumari

Rendered from Affymetrix.Rmd in GWASTools 1.53.0.
Introduction to qsvaRUpdated 1 years ago

Joshua M. Stolz, Hedia Tnani, Leonardo Collado-Torres

Rendered from Intro_qsvaR.Rmd in qsvaR 1.11.0.
MSstatsPTM TMT WorkflowUpdated 1 years ago

Devon Kohler ([email protected])

Rendered from MSstatsPTM_TMT_Workflow.Rmd in MSstatsPTM 2.9.0.
gcat PackageUpdated 1 years ago

Alejandro Ochoa

Rendered from gcatest.Rnw in gcatest 2.7.0.
lfa PackageUpdated 1 years ago

Alejandro Ochoa

Rendered from lfa.Rnw in lfa 2.7.0.
Tools for IMC data analysisUpdated 1 years ago

Nils Eling, Lasse Meyer, Daniel Schulz

Rendered from imcRtools.Rmd in imcRtools 1.13.0.
edgeR User's GuideUpdated 1 years ago

Yunshun Chen

Rendered from edgeRUsersGuide.Rnw in edgeR 4.5.0.
limma User's GuideUpdated 1 years ago

Gordon Smyth

Rendered from usersguide.Rnw in limma 3.63.2.
How to find Total RNA Expression Genes (TREGs)Updated 1 years ago

Louise A. Huuki-Myers, Leonardo Collado-Torres

Rendered from finding_Total_RNA_Expression_Genes.Rmd in TREG 1.11.0.
EBSeq VignetteUpdated 1 years ago

Xiuyu Ma

Rendered from EBSeq_Vignette.Rnw in EBSeq 2.5.0.
Introduction to iSEEindexUpdated 1 years ago

Kevin Rue-Albrecht

Rendered from iSEEindex.Rmd in iSEEindex 1.5.0.
A brief introduction to limmaUpdated 1 years ago

Gordon Smyth

Rendered from intro.Rmd in limma 3.63.2.
Scanning sequences for miRNA binding sites and exploring matches with scanMiRUpdated 1 years ago

Fridolin Gross, Pierre-Luc Germain, Michael Soutschek

Rendered from scanning.Rmd in scanMiR 1.13.0.
Maaslin2Updated 1 years ago

Himel Mallick, Ali Rahnavard, Lauren McIver

Rendered from maaslin2.Rmd in Maaslin2 1.21.0.
How to Assemble a chromLocation ObjectUpdated 1 years ago

Robert Gentleman, Rohit Satyam

Rendered from byChroms.Rmd in geneplotter 1.85.0.
02 Working with larger VCF: T2T by chromosomeUpdated 1 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from large_t2t.Rmd in BiocHail 1.7.1.
HiCcompare VignetteUpdated 1 years ago

John Stansfield, Mikhail Dozmorov

Rendered from HiCcompare-vignette.Rmd in HiCcompare 1.29.0.
Introduction to VariantAnnotation Updated 1 years ago

Valerie Obenchain

Rendered from VariantAnnotation.Rmd in VariantAnnotation 1.53.0.
Using filterVcf() to Select Variants from VCF Files Updated 1 years ago

Paul Shannon

Rendered from filterVcf.Rmd in VariantAnnotation 1.53.0.
miaSim: Microbiome Data SimulationUpdated 1 years ago

miaSim authors

Rendered from miaSim.Rmd in miaSim 1.13.0.
HarmonizR_VignetteUpdated 1 years ago

Simon Schlumbohm

Rendered from HarmonizR_Vignette.Rmd in HarmonizR 1.5.0.
Clustering Deviation Index (CDI) TutorialUpdated 1 years ago

Jiyuan Fang, Jichun Xie

Rendered from CDI.Rmd in CDI 1.5.0.
The waddR packageUpdated 1 years ago

Julian Flesch

Rendered from waddR.Rmd in waddR 1.21.0.
cfdnakit vignetteUpdated 1 years ago

Pitithat Puranachot

Rendered from cfdnakit-vignette.Rmd in cfdnakit 1.5.0.
Vignette for pfamAnalyzeRUpdated 2 years ago

Kristoffer Vitting-Seerup

Rendered from pfamAnalyzeR.Rmd in pfamAnalyzeR 1.7.0.
Full power GenomicDistributionsUpdated 2 years ago

Nathan Sheffield

Rendered from full-power.Rmd in GenomicDistributions 1.15.0.
TCGAbiolinks: Searching GDC databaseUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from query.Rmd in TCGAbiolinks 2.35.0.
TCGAbiolinks: Clinical dataUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from clinical.Rmd in TCGAbiolinks 2.35.0.
Rounding numeric valuesUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from rounding.Rmd in iSEEde 1.5.0.
Supported differential expression methodsUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from methods.Rmd in iSEEde 1.5.0.
Using annotations to facilitate interactive explorationUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from annotations.Rmd in iSEEde 1.5.0.
scmap package vignetteUpdated 2 years ago

Vladimir Kiselev and Martin Hemberg

Rendered from scmap.Rmd in scmap 1.29.0.
RBGL: R interface to boost graph libraryUpdated 2 years ago

L. Long, VJ Carey, R. Gentleman, Emmanuel Taiwo

Rendered from RBGL.Rmd in RBGL 1.83.0.
distinct: a method for differential analyses via hierarchical permutation testsUpdated 2 years ago

Simone Tiberi

Rendered from distinct.Rmd in distinct 1.19.0.
Getting started with ISAnalyticsUpdated 2 years ago

Giulia Pais

Rendered from ISAnalytics.Rmd in ISAnalytics 1.17.0.
TCGAbiolinks: Searching, downloading and visualizing mutation filesUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from mutation.Rmd in TCGAbiolinks 2.35.0.
Analyzing and visualizing TCGA dataUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from analysis.Rmd in TCGAbiolinks 2.35.0.
3.2 - Identifying differentially methylated probesUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from analysis_diff_meth.Rmd in ELMER 2.31.0.
3.3 - Identifying putative probe-gene pairsUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from analysis_get_pair.Rmd in ELMER 2.31.0.
3.4 - Motif enrichment analysis on the selected probesUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from analysis_motif_enrichment.Rmd in ELMER 2.31.0.
3.5 - Identifying regulatory TFsUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from analysis_regulatory_tf.Rmd in ELMER 2.31.0.
4.4 - Regulatory TF plotsUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from plots_TF.Rmd in ELMER 2.31.0.
megadepth quick start guideUpdated 2 years ago

David Zhang, Leonardo Collado-Torres

Rendered from megadepth.Rmd in megadepth 1.17.0.
Introduction to derfinderPlotUpdated 2 years ago

Leonardo Collado-Torres

Rendered from derfinderPlot.Rmd in derfinderPlot 1.41.0.
Introduction to derfinderHelperUpdated 2 years ago

Leonardo Collado-Torres

Rendered from derfinderHelper.Rmd in derfinderHelper 1.41.0.
TCGAbiolinks: Downloading and preparing files for analysisUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from download_prepare.Rmd in TCGAbiolinks 2.35.0.
recount3 quick start guideUpdated 2 years ago

Leonardo Collado-Torres

Rendered from recount3-quickstart.Rmd in recount3 1.17.0.
Compilation of TCGA molecular subtypesUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from subtypes.Rmd in TCGAbiolinks 2.35.0.
seqArchRplus facilitates downstream analysis of clusters of promoter sequence architecturesUpdated 2 years ago

Sarvesh Nikumbh

Rendered from seqArchRplus.Rmd in seqArchRplus 1.7.0.
VDJdive WorkflowUpdated 2 years ago

Kelly Street, Mercedeh Movassagh, Jill Lundell

Rendered from workflow.Rmd in VDJdive 1.9.0.
Importing dataUpdated 2 years ago

Haakon Tjeldnes & Kornel Labun

Rendered from Importing_Data.Rmd in ORFik 1.27.0.
splots: visualization of data from assays in microtitre plate or slide formatUpdated 2 years ago

Wolfgang Huber

Rendered from splots.Rmd in splots 1.73.0.
Identify locally aneuploid cells from scRNA-seq using partCNVUpdated 2 years ago

Ziyi Li, Ruoxing Li

Rendered from partCNV_vignette.Rmd in partCNV 1.5.0.
ampliCan FAQUpdated 2 years ago

Kornel Labun & Eivind Valen

Rendered from amplicanFAQ.Rmd in amplican 1.29.0.
Report breakdown by amplicon sequenceUpdated 2 years ago

ampliCan

Rendered from example_amplicon_report.Rmd in amplican 1.29.0.
Report breakdown by barcodeUpdated 2 years ago

ampliCan

Rendered from example_barcode_report.Rmd in amplican 1.29.0.
Report breakdown by IDUpdated 2 years ago

ampliCan

Rendered from example_id_report.Rmd in amplican 1.29.0.
Summary Read ReportUpdated 2 years ago

ampliCan

Rendered from example_index.Rmd in amplican 1.29.0.
rifiComparativeUpdated 2 years ago

Loubna Youssar

Rendered from rifiComparative.Rmd in rifiComparative 1.7.0.
ReactomeContentService4R: an R Interface for the Reactome Content ServiceUpdated 2 years ago

Chi-Lam Poon

Rendered from ReactomeContentService4R.Rmd in ReactomeContentService4R 1.15.0.
ReactomeGraph4R: an R Interface for the Reactome Graph DatabaseUpdated 2 years ago

Chi-Lam Poon

Rendered from Introduction.Rmd in ReactomeGraph4R 1.15.0.
User GuideUpdated 2 years ago

Søren Helweg Dam

Rendered from User-Guide.Rmd in pairedGSEA 1.7.0.
Secondary analyses of CNV data (HRD and more) with oncoscanRUpdated 2 years ago

Yann Christinat

Rendered from oncoscanR.Rmd in oncoscanR 1.9.0.
Introduction to HiContactsUpdated 2 years ago

Jacques Serizay

Rendered from HiContacts.Rmd in HiContacts 1.9.0.
pogos -- PharmacOGenomics Ontology SupportUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from pogos.Rmd in pogos 1.27.0.
MSstatsShiny Launch InstructionsUpdated 2 years ago

Devon Kohler ([email protected])

Rendered from MSstatsShiny_Launch_Instructions.Rmd in MSstatsShiny 1.9.0.
Differential Composition Analysis with DCATSUpdated 2 years ago

Xinyi LIN

Rendered from Intro_to_DCATS.Rmd in DCATS 1.5.0.
Interoptability between MAST and SingleCellExperiment-derived packages.Updated 2 years ago

Andrew McDavid

Rendered from MAST-interoperability.Rmd in MAST 1.33.0.
Introduction to marinerUpdated 2 years ago

Eric Davis

Rendered from introduction_to_mariner.Rmd in mariner 1.7.0.
Using scTHIUpdated 2 years ago

Michele Ceccarelli, Francesca Pia Caruso

Rendered from vignette.Rmd in scTHI 1.19.0.
SVMDO-TutorialUpdated 2 years ago

Author: Mustafa Erhan Özer

Rendered from SVMDO_guide.Rmd in SVMDO 1.7.0.
SEESAW - Allelic expression analysis with Salmon and SwishUpdated 2 years ago

Michael Love

Rendered from allelic.Rmd in fishpond 2.13.0.
The Xeva User's GuideUpdated 2 years ago

Benjamin Haibe-Kains

Rendered from Xeva.Rnw in Xeva 1.23.0.
OutSpliceUpdated 2 years ago

Joseph Bendik, Sandhya Kalavacherla, Michael Considine, Bahman Afsari, Michael F. Ochs, Joseph Califano, Daria A. Gaykalova, Elana Fertig, Theresa Guo

Rendered from OutSplice.Rmd in OutSplice 1.7.0.
OrganismDbi: A meta framework for Annotation PackagesUpdated 2 years ago

Marc Carlson, Aliyu Atiku Mustapha

Rendered from OrganismDbi.Rmd in OrganismDbi 1.49.0.
Introduction to MicrobiomeProfilerUpdated 2 years ago

Meijun Chen and GuangChuang Yu

Rendered from MicrobiomeProfiler.Rmd in MicrobiomeProfiler 1.13.0.
Introduction to stJoincountUpdated 2 years ago

Jiarong Song

Rendered from stJoincount-vignette.Rmd in stJoincount 1.9.0.
SCBN TutorialUpdated 2 years ago

Yan Zhou

Rendered from SCBN.Rmd in SCBN 1.25.0.
FeatSeekR user guideUpdated 2 years ago

Tuemay Capraz

Rendered from FeatSeekR-vignette.Rmd in FeatSeekR 1.7.0.
mastR: Markers Automated Screening Tool in RUpdated 2 years ago

Jinjin Chen, Ahmed Mohamed, Chin Wee Tan

Rendered from mastR_Demo.Rmd in mastR 1.7.0.
IntroductionUpdated 2 years ago

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered from v1_introduction.Rmd in VERSO 1.17.0.
Running VERSOUpdated 2 years ago

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered from v2_running_VERSO.Rmd in VERSO 1.17.0.
IntroductionUpdated 2 years ago

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered from v1_introduction.Rmd in LACE 2.11.0.
LACE-interfaceUpdated 2 years ago

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered from v3_LACE_interface.Rmd in LACE 2.11.0.
Running LACEUpdated 2 years ago

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered from v2_running_LACE.Rmd in LACE 2.11.0.
MEB TutorialUpdated 2 years ago

Yan Zhou, Jiadi Zhu

Rendered from NIMEB.Rmd in MEB 1.21.0.
An Introduction To ngsReportsUpdated 2 years ago

Christopher Ward, Hien To, Stevie Pederson

Rendered from ngsReportsIntroduction.Rmd in ngsReports 2.9.0.
Tranferable Omics PedictionUpdated 2 years ago

Harry Robertson, Nicholas Robertson, Ellis Patrick

Rendered from BuildingATOPModel.Rmd in TOP 1.7.0.
Authoring R Markdown vignettesUpdated 2 years ago

Andrzej Oleś, Wolfgang Huber, Martin Morgan

Rendered from AuthoringRmdVignettes.Rmd in BiocStyle 2.35.0.
extraChIPs: Range-Based operationsUpdated 2 years ago

Stevie Pederson

Rendered from range_based_functions.Rmd in extraChIPs 1.11.0.
Some Basic Analysis of ChIP-Seq DataUpdated 2 years ago

Oluwabukola Bamigbade

Rendered from Workflow.Rmd in chipseq 1.57.0.
Introduction to iSEEdeUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from iSEEde.Rmd in iSEEde 1.5.0.
CAEN TutorialUpdated 2 years ago

Yan Zhou

Rendered from CAEN.Rmd in CAEN 1.15.0.
Combine LC-MS Metabolomics Datasets with metabCombinerUpdated 2 years ago

Hani Habra

Rendered from metabCombiner_vignette.Rmd in metabCombiner 1.17.0.
hotSPOT-vignetteUpdated 2 years ago

Sydney Grant, Lei Wei, Gyorgy Paragh

Rendered from hotSPOT-vignette.Rmd in seq.hotSPOT 1.7.0.
MultimodalExperimentUpdated 2 years ago

Lucas Schiffer

Rendered from MultimodalExperiment.Rmd in MultimodalExperiment 1.7.0.
DNAfusion \vspace{0.5in}Updated 2 years ago

Christoffer Trier Maansson, Emma Roger Andersen

Rendered from Introduction_to_DNAfusion.Rmd in DNAfusion 1.9.0.
SpotClean adjusts for spot swapping in spatial transcriptomics dataUpdated 2 years ago

Zijian Ni and Christina Kendziorski

Rendered from SpotClean.Rmd in SpotClean 1.9.0.
IntroductionUpdated 2 years ago

Daniele Ramazzotti, Avantika Lal, Keli Liu, Luca De Sano, Robert Tibshirani, Arend Sidow

Rendered from v1_introduction.rmd in SparseSignatures 2.17.0.
Using the packageUpdated 2 years ago

Daniele Ramazzotti, Avantika Lal, Keli Liu, Luca De Sano, Robert Tibshirani, Arend Sidow

Rendered from v2_using_the_package.rmd in SparseSignatures 2.17.0.
Detecting and correcting batch effects with BEclearUpdated 2 years ago

Livia Rasp, Markus Merl

Rendered from BEclear.Rmd in BEclear 2.23.0.
SCFA package manualUpdated 2 years ago

Duc Tran

Rendered from Example.Rmd in SCFA 1.17.0.
The Rmmquant packageUpdated 2 years ago

Matthias Zytnicki

Rendered from Rmmquant.Rmd in Rmmquant 1.25.0.
DAMEfinder WorkflowUpdated 2 years ago

Stephany Orjuela, Dania Machlab, Mark Robinson

Rendered from DAMEfinder_workflow.Rmd in DAMEfinder 1.19.0.
RiboCryptOverviewUpdated 2 years ago

Michal Swirski & Hakon Tjeldnes

Rendered from RiboCrypt_overview.rmd in RiboCrypt 1.13.0.
Setting up the workflow and first stepsUpdated 2 years ago

Giulia Pais

Rendered from workflow_start.Rmd in ISAnalytics 1.17.0.
An Introduction to RsamtoolsUpdated 2 years ago

Martin Morgan, Samuel Busayo

Rendered from Rsamtools-Overview.Rmd in Rsamtools 2.23.0.
cmapR TutorialUpdated 2 years ago

Ted Natoli

Rendered from tutorial.Rmd in cmapR 1.19.0.
Understanding protein groups with adjacency matricesUpdated 2 years ago

Laurent Gatto

Rendered from AdjacencyMatrix.Rmd in PSMatch 1.11.0.
Processing quantitative metabolomics data with the qmtools packageUpdated 2 years ago

Jaehyun Joo

Rendered from qmtools.Rmd in qmtools 1.11.0.
Slingshot: Trajectory Inference for Single-Cell DataUpdated 2 years ago

Kelly Street

Rendered from vignette.Rmd in slingshot 2.15.0.
MassBank Data for AnnotationHubUpdated 2 years ago

Johannes Rainer

Rendered from creating-MassBank-CompDbs.Rmd in AHMassBank 1.7.0.
A quick start guide to the standR packageUpdated 2 years ago

Ning Liu, Dharmesh Bhuva, Ahmed Mohamed, Chin Wee Tan, Melissa Davis

Rendered from Quick_start.Rmd in standR 1.11.0.
Using the genefilter function to filter genes from a microarray datasetUpdated 2 years ago

Khadijah Amusat

Rendered from howtogenefilter.Rmd in genefilter 1.89.0.
Introduction to HPiPUpdated 2 years ago

Matineh Rahmatbakhsh

Rendered from HPiP_tutorial.Rmd in HPiP 1.13.0.
Introduction to the netresponse R packageUpdated 2 years ago

Leo Lahti et al.

Rendered from NetResponse.Rmd in netresponse 1.67.0.
DELocalUpdated 2 years ago

Rishi Das Roy

Rendered from DELocal.Rmd in DELocal 1.7.0.
COSMOS-tutorialUpdated 2 years ago

A. Dugourd, A. Gabor and K. Zirngibl

Rendered from tutorial.Rmd in cosmosR 1.15.0.
Data AnalysesUpdated 2 years ago

Sean K. Maden, Reid F. Thompson, Kasper D. Hansen, Abhinav Nellore

Rendered from recountmethylation_data_analyses.Rmd in recountmethylation 1.17.0.
Nearest neighbors analysis for DNAm arraysUpdated 2 years ago

Sean K. Maden

Rendered from recountmethylation_search_index.Rmd in recountmethylation 1.17.0.
Working with DNAm data typesUpdated 2 years ago

Sean K. Maden

Rendered from exporting_saving_data.Rmd in recountmethylation 1.17.0.
recountmethylation User's GuideUpdated 2 years ago

Sean K. Maden, Reid F. Thompson, Kasper D. Hansen, Abhinav Nellore

Rendered from recountmethylation_users_guide.Rmd in recountmethylation 1.17.0.
EnrichmentUpdated 2 years ago

Y-h. Taguchi

Rendered from Enrichment.Rmd in TDbasedUFEadv 1.7.0.
How to use TDbasedUFEadvUpdated 2 years ago

Y-h. Taguchi

Rendered from How_to_use_TDbasedUFEadv.Rmd in TDbasedUFEadv 1.7.0.
Errors, Logs and Debugging Updated 2 years ago

Martin Morgan

Rendered from Errors_Logs_And_Debugging.Rnw in BiocParallel 1.41.0.
Explanation of TDbasedUFEadvUpdated 2 years ago

Y-h. Taguchi

Rendered from Explanation_of_TDbasedUFEadv.Rmd in TDbasedUFEadv 1.7.0.
MOFA2: training a model in RUpdated 2 years ago

Ricard Argelaguet, Britta Velten

Rendered from getting_started_R.Rmd in MOFA2 1.17.0.
QuickStartUpdated 2 years ago

Y-h. Taguchi

Rendered from QuickStart.Rmd in TDbasedUFE 1.7.0.
TDbasedUFEUpdated 2 years ago

Y-h. Taguchi

Rendered from TDbasedUFE.Rmd in TDbasedUFE 1.7.0.
Make Enriched HeatmapsUpdated 2 years ago

Zuguang Gu ( [email protected] )

Rendered from EnrichedHeatmap.Rmd in EnrichedHeatmap 1.37.0.
Visualize Categorical SignalsUpdated 2 years ago

Zuguang Gu ( [email protected] )

Rendered from visualize_categorical_signals_wrapper.Rmd in EnrichedHeatmap 1.37.0.
Compare row ordering methodsUpdated 2 years ago

Zuguang Gu ( [email protected] )

Rendered from row_odering.Rmd in EnrichedHeatmap 1.37.0.
Visualize Comprehensive Associations in Roadmap datasetUpdated 2 years ago

Zuguang Gu ( [email protected] )

Rendered from roadmap.Rmd in EnrichedHeatmap 1.37.0.
Introduction to GenomicFilesUpdated 2 years ago

Valerie Obenchain, Michael Love, Martin Morgan, Sonali Kumari

Rendered from GenomicFiles.Rmd in GenomicFiles 1.43.0.
About BioCorUpdated 2 years ago

Lluís Revilla, Juan José Lozano, Pau Sancho-Bru

Rendered from BioCor_1_basics.Rmd in BioCor 1.31.0.
Advanced usage of BioCorUpdated 2 years ago

Lluís Revilla, Juan José Lozano, Pau Sancho-Bru

Rendered from BioCor_2_advanced.Rmd in BioCor 1.31.0.
How to find genes whose expression profile is similar to that of specified genesUpdated 2 years ago

Emmanuel Taiwo

Rendered from howtogenefinder.Rmd in genefilter 1.89.0.
ArrayExpress: Import and convert ArrayExpress data sets into R objectUpdated 2 years ago

Jose Marugan

Rendered from ArrayExpress.Rnw in ArrayExpress 1.67.0.
Complete Guide to cytofQCUpdated 2 years ago

Jill Lundell

Rendered from cytofQC.Rmd in cytofQC 1.7.0.
rWikiPathways and RCy3Updated 2 years ago

by Alexander Pico

Rendered from rWikiPathways-and-RCy3.Rmd in rWikiPathways 1.27.0.
EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq dataUpdated 2 years ago

Juan P. Romero, Juan A. Ferrer-Bonsoms & Angel Rubio

Rendered from EventPointer.Rmd in EventPointer 3.15.0.
flowGateUpdated 2 years ago

Andrew Wight

Rendered from flowGate.Rmd in flowGate 1.7.0.
Description and usage of MsBackendMassbankUpdated 2 years ago

RforMassSpectrometry Package Maintainer

Rendered from MsBackendMassbank.Rmd in MsBackendMassbank 1.15.0.
scvi-tools CITE-seq tutorial in R, using serialized tutorial componentsUpdated 2 years ago

Follows scvi-tools doc, Gayoso, Steier et al. DOI 10.1038/s41592-020-01050-x

Rendered from citeseq_tut.Rmd in scviR 1.7.0.
scviR: an R package interfacing Bioconductor and scvi-toolsUpdated 2 years ago

Vince Carey stvjc at channing.harvard.edu

Rendered from scviR.Rmd in scviR 1.7.0.
Ribo-seq pipelineUpdated 2 years ago

Haakon Tjeldnes & Kornel Labun

Rendered from Ribo-seq_pipeline.Rmd in ORFik 1.27.0.
Tutorial: Download histology images from the Human Protein Atlas Updated 2 years ago

Anh N. Tran

Rendered from f_HPAanalyze_case_images.Rmd in HPAanalyze 1.25.0.
EpiCompare: Getting startedUpdated 2 years ago

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered from EpiCompare.Rmd in EpiCompare 1.11.0.
Example reportUpdated 2 years ago

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered from example_report.Rmd in EpiCompare 1.11.0.
Analyzing NanoString nCounter Data with the NanoTubeUpdated 2 years ago

Caleb A Class

Rendered from NanoTube.Rmd in NanoTube 1.13.0.
Scalable Generalized Mixed Models in PheWAS using SAIGEgdsUpdated 2 years ago

Xiuwen Zheng (Genomics Research Center, AbbVie, North Chicago, US)

Rendered from SAIGEgds.Rmd in SAIGEgds 2.7.1.
Using the sangerseqR packageUpdated 2 years ago

Jonathon T. Hill, PhD

Rendered from sangerseqRWalkthrough.Rmd in sangerseqR 1.43.0.
Differential cell-type-specific allelic imbalance with airpartUpdated 2 years ago

Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love

Rendered from airpart.Rmd in airpart 1.15.0.
biocthis developer notesUpdated 2 years ago

Leonardo Collado-Torres

Rendered from biocthis_dev_notes.Rmd in biocthis 1.17.0.
Introduction to sequence motifsUpdated 2 years ago

Benjamin Jean-Marie Tremblay^[[email protected]]

Rendered from IntroductionToSequenceMotifs.Rmd in universalmotif 1.25.1.
The Netboost users guideUpdated 2 years ago

Pascal Schlosser, Jochen Knaus

Rendered from netboost.Rmd in netboost 2.15.0.
rifiUpdated 2 years ago

Walja Wanney, Loubna Youssar and Jens Georg

Rendered from vignette.Rmd in rifi 1.11.0.
Pseudobulk and differential expressionUpdated 2 years ago

Constantin Ahlmann-Eltze

Rendered from pseudobulk.Rmd in glmGamPoi 1.19.0.
LEA: An R Package for Landscape and Ecological Association StudiesUpdated 2 years ago

Olivier Francois

Rendered from LEA.Rnw in LEA 3.19.1.
IsoformSwitchAnalyzeRUpdated 2 years ago

Kristoffer Vitting-Seerup

Rendered from IsoformSwitchAnalyzeR.Rmd in IsoformSwitchAnalyzeR 2.7.0.
Retrofit Colon VignetteUpdated 2 years ago

Adam Keebum Park, Roopali Singh

Rendered from ColonVignette.Rmd in retrofit 1.7.0.
Retrofit Simulation VignetteUpdated 2 years ago

Adam Keebum Park, Roopali Singh

Rendered from SimulationVignette.Rmd in retrofit 1.7.0.
BiocHubsShiny: Interactive Display of Hub ResourcesUpdated 2 years ago

Marcel Ramos, Vincent J. Carey

Rendered from BiocHubsShiny.Rmd in BiocHubsShiny 1.7.1.
An introduction to GSEABaseUpdated 2 years ago

Martin Morgan, Paul Villafuerte

Rendered from GSEABase.Rmd in GSEABase 1.69.0.
Single Cell ATAC-seq Analysis with CiceroUpdated 2 years ago

Hannah Pliner

Rendered from website.Rmd in cicero 1.25.0.
Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze Updated 2 years ago

Anh N. Tran

Rendered from a_HPAanalyze_quick_start.Rmd in HPAanalyze 1.25.0.
In-depth: Working with Human Protein Atlas (HPA) data in R with HPAanalyze Updated 2 years ago

Anh N. Tran

Rendered from b_HPAanalyze_indepth.Rmd in HPAanalyze 1.25.0.
Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries Updated 2 years ago

Anh N. Tran

Rendered from c_HPAanalyze_case_query.Rmd in HPAanalyze 1.25.0.
Tutorial: Working with Human Protein Atlas (HPA) xml files offline Updated 2 years ago

Anh N. Tran

Rendered from d_HPAanalyze_case_offline_xml.Rmd in HPAanalyze 1.25.0.
Tutorial: Export Human Protein Atlas (HPA) data as JSON Updated 2 years ago

Anh N. Tran

Rendered from e_HPAanalyze_case_json.Rmd in HPAanalyze 1.25.0.
Code for figures from HPAanalyze paper Updated 2 years ago

Anh N. Tran

Rendered from z_HPAanalyze_paper_figures.Rmd in HPAanalyze 1.25.0.
Getting startedUpdated 2 years ago

Authors: Alan Murphy, Brian Schilder, and Nathan Skene

Rendered from EWCE.Rmd in EWCE 1.15.0.
Introduction to CellBenchUpdated 2 years ago

Shian Su

Rendered from Introduction.Rmd in CellBench 1.23.0.
GeoTcgaDataUpdated 2 years ago

Erqiang Hu

Rendered from GeoTcgaData.Rmd in GeoTcgaData 2.7.0.
magpie Package User's GuideUpdated 2 years ago

Daoyu Duan, Zhenxing Guo

Rendered from magpie.Rmd in magpie 1.7.0.
HiCoolUpdated 2 years ago

Jacques Serizay

Rendered from HiCool.Rmd in HiCool 1.7.0.
An R package for prediction of nucleosome positioningUpdated 2 years ago

Hiroaki Kato

Rendered from nuCpos-intro.Rnw in nuCpos 1.25.0.
Dimension reduction of single cell data with corralUpdated 2 years ago

Lauren Hsu, Aedin Culhane

Rendered from corral_dimred.Rmd in corral 1.17.0.
Creating A Hub Package: ExperimentHub or AnnotationHubUpdated 2 years ago

Valerie Obenchain, Lori Shepherd, and Kayla Interdonato

Rendered from CreateAHubPackage.Rmd in HubPub 1.15.0.
Main vignette:Playing with networks using CNORfeederUpdated 2 years ago

Attila Gabor

Rendered from CNORfeeder-vignette.Rnw in CNORfeeder 1.47.0.
\texttt{flagme}: Fragment-level analysis of \ GC-MS-based metabolomics dataUpdated 2 years ago

Mark Robinson

Rendered from flagme.Rnw in flagme 1.63.0.
Using flagme -- Fragment-level analysis of GC-MS-based metabolomics dataUpdated 2 years ago

Mark Robinson

Rendered from flagme-knitr.Rnw in flagme 1.63.0.
A working Demo for synletUpdated 2 years ago

Chunxuan Shao

Rendered from synlet-vignette.Rmd in synlet 2.7.0.
A transfer learning algorithm for spatial proteomicsUpdated 2 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v05-pRoloc-transfer-learning.Rmd in pRoloc 1.47.0.
mslpUpdated 2 years ago

Chunxuan Shao

Rendered from mslp.Rmd in mslp 1.9.0.
Using the MassSpecWavelet packageUpdated 2 years ago

Pan Du, Warren A. Kibbe, Simon Lin

Rendered from MassSpecWavelet.Rmd in MassSpecWavelet 1.73.0.
App TutorialUpdated 2 years ago

Michal Swirski & Hakon Tjeldnes

Rendered from RiboCrypt_app_tutorial.rmd in RiboCrypt 1.13.0.
An introduction to the RESOLVE R packageUpdated 2 years ago

Luca De Sano, Daniele Ramazzotti

Rendered from RESOLVE.rmd in RESOLVE 1.9.0.
Assessing genome assembly and annotation qualityUpdated 2 years ago

Fabricio Almeida-Silva, Yves Van de Peer

Rendered from vignette_01_assessing_genome_assembly.Rmd in cogeqc 1.11.0.
Extended examplesUpdated 2 years ago

Authors: Alan Murphy, Brian Schilder, and Nathan Skene

Rendered from extended.Rmd in EWCE 1.15.0.
Umbrella for the alabaster frameworkUpdated 2 years ago

Aaron Lun

Rendered from userguide.Rmd in alabaster 1.7.0.
An Overview of the BiocIO packageUpdated 2 years ago

Daniel Van Twisk, Martin Morgan

Rendered from BiocIO.Rmd in BiocIO 1.17.1.
EDIRqueryUpdated 2 years ago

Laura D.T. Vo Ngoc

Rendered from EDIRquery.Rmd in EDIRquery 1.7.0.
Creating a pool set for matchRangesUpdated 2 years ago

Eric S. Davis

Rendered from matching_pool_set.Rmd in nullranges 1.13.0.
Introduction to MutationalPatternsUpdated 2 years ago

Freek Manders, Francis Blokzijl, Roel Janssen, Rurika Oka, Jurrian de Kanter, Mark van Roosmalen, Ruben van Boxtel, Edwin Cuppen

Rendered from Introduction_to_MutationalPatterns.Rmd in MutationalPatterns 3.17.0.
Metadata schemas for Bioconductor objectsUpdated 2 years ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.schemas 1.7.0.
BG2Updated 2 years ago

Shuangshuang Xu, Jacob Williams, and Marco A.R. Ferreira

Rendered from BG2.Rmd in BG2 1.7.0.
Using the GADGETS method to detect epistatic maternally-mediated effects and maternal-fetal interactionsUpdated 2 years ago

Michael Nodzenski

Rendered from Including_Maternal_SNPs.Rmd in epistasisGA 1.9.0.
Detecting GxGxE interactions with case-parent triads using E-GADGETSUpdated 2 years ago

Michael Nodzenski

Rendered from E_GADGETS.Rmd in epistasisGA 1.9.0.
An introduction to miQCUpdated 2 years ago

Ariel Hippen and Stephanie Hicks

Rendered from miQC.Rmd in miQC 1.15.0.
clevRvis VignetteUpdated 2 years ago

Sarah Sandmann

Rendered from clevRvis.Rmd in clevRvis 1.7.0.
Comprehensive DNA Methylation Analysis with RnBeadsUpdated 2 years ago

Fabian Mueller

Rendered from RnBeads.Rnw in RnBeads 2.25.0.
IntEREstUpdated 2 years ago

Ali Oghabian

Rendered from IntEREst.Rmd in IntEREst 1.31.0.
Borealis outlier methylation detectionUpdated 2 years ago

Gavin Oliver, Garrett Jenkinson, Eric Klee

Rendered from borealis.Rmd in borealis 1.11.0.
Introduction to nullrangesUpdated 2 years ago

Michael Love

Rendered from nullranges.Rmd in nullranges 1.13.0.
AMARETTOUpdated 2 years ago

Jayendra Shinde1, Celine Everaert2, Shaimaa Bakr1, Mohsen Nabian2, Jishu Xu2,Vincent Carey2, Nathalie Pochet2, Olivier Gevaert1**1 Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine and Biomedical Data Science, 1265 Welch Rd, Stanford, CA, USA 2 Brigham and Women's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard, Boston and Cambridge, MA, USA [email protected] **[email protected]

Rendered from amaretto.Rmd in AMARETTO 1.23.0.
Extending the RCX Data Model Updated 2 years ago

Florian J. Auer

Rendered from Extending_the_RCX_Data_Model.Rmd in RCX 1.11.0.
Introduction to crisprDesignUpdated 2 years ago

Jean-Philippe Fortin, Luke Hoberecht

Rendered from intro.Rmd in crisprDesign 1.9.0.
KEGGgraph: Application ExamplesUpdated 2 years ago

Jitao David Zhang

Rendered from KEGGgraphApp.Rnw in KEGGgraph 1.67.0.
KEGGgraph: graph approach to KEGG PATHWAYUpdated 2 years ago

Jitao David Zhang

Rendered from KEGGgraph.Rnw in KEGGgraph 1.67.0.
PeacoQCUpdated 2 years ago

Annelies Emmaneel

Rendered from PeacoQC_Vignette.Rmd in PeacoQC 1.17.0.
Submitting your organism to GenomeInfoDbUpdated 2 years ago

Sonali Arora, H. Khan

Rendered from Accept-organism-for-GenomeInfoDb.Rmd in GenomeInfoDb 1.43.1.
Modeling spatially resolved omics with mistyRUpdated 2 years ago

Jovan Tanevski

Rendered from mistyR.Rmd in mistyR 1.15.0.
protGear vignette processing suiteUpdated 2 years ago

Kennedy Mwai

Rendered from vignette.Rmd in protGear 1.11.0.
Charge and Hydropathy VignetteUpdated 2 years ago

William M. McFadden

Rendered from chargeHydropathy-vignette.Rmd in idpr 1.17.0.
idpr Package Overview VignetteUpdated 2 years ago

William McFadden

Rendered from idpr-vignette.Rmd in idpr 1.17.0.
IUPred VignetteUpdated 2 years ago

William McFadden

Rendered from iupred-vignette.Rmd in idpr 1.17.0.
Sequence Map VignetteUpdated 2 years ago

William M. McFadden

Rendered from sequenceMAP-vignette.Rmd in idpr 1.17.0.
Structural Tendency VignetteUpdated 2 years ago

William McFadden

Rendered from structuralTendency-vignette.Rmd in idpr 1.17.0.
brendaDbUpdated 2 years ago

Yi Zhou

Rendered from brendaDb.Rmd in brendaDb 1.21.0.
Checking gene expression signatures against random and known signatures with SigCheckUpdated 2 years ago

Rory Stark

Rendered from SigCheck.Rnw in SigCheck 2.39.0.
Prepare Peptide Spectrum Matches for Use in Targeted ProteomicsUpdated 2 years ago

Christian Panse, Christian Trachsel, Jonas Grossmann, Witold E. Wolski

Rendered from specL.Rmd in specL 1.41.0.
immunoClust packageUpdated 2 years ago

Till Soerensen

Rendered from immunoClust.Rnw in immunoClust 1.39.2.
Ten Things You Didn't Know (slides from BioC 2016) Updated 2 years ago

Hervé Pagès

Rendered from Ten_things_slides.Rnw in GenomicRanges 1.59.1.
specL automatic reportUpdated 2 years ago

Christian Panse, Witold E. Wolski

Rendered from report.Rmd in specL 1.41.0.
Rle Tips and TricksUpdated 2 years ago

Patrick Aboyoun, Beryl Kanali

Rendered from RleTricks.Rmd in S4Vectors 0.45.2.
graphBAM and MultiGraph classesUpdated 2 years ago

N. Gopalakrishnan, Halimat C. Atanda

Rendered from MultiGraphClass.Rmd in graph 1.85.0.
speckle: statistical methods for analysing single cell RNA-seq dataUpdated 2 years ago

Belinda Phipson

Rendered from speckle.Rmd in speckle 1.7.0.
Basic analyses with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from basic_analysis.Rmd in SPIAT 1.9.0.
Characterising tissue structure with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from tissue-structure.Rmd in SPIAT 1.9.0.
Identifying cellular neighborhood with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from neighborhood.Rmd in SPIAT 1.9.0.
Overview of the SPIAT packageUpdated 2 years ago

Anna Trigos, Yuzhou Feng, Tianpei Yang, Mabel Li, John Zhu, Volkan Ozcoban, Maria Doyle

Rendered from SPIAT.Rmd in SPIAT 1.9.0.
Quality control and visualisation with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from quality-control_visualisation.Rmd in SPIAT 1.9.0.
Reading in data and data formatting in SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from data_reading-formatting.Rmd in SPIAT 1.9.0.
Spatial heterogeneity with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from spatial-heterogeneity.Rmd in SPIAT 1.9.0.
deconvR : Simulation and Deconvolution of Omic ProfilesUpdated 2 years ago

Irem B. Gunduz, Veronika Ebenal, Altuna Akalin

Rendered from deconvRVignette.Rmd in deconvR 1.13.0.
Use of the GADGETS method to identify multi-SNP effects in nuclear familiesUpdated 2 years ago

Michael Nodzenski

Rendered from GADGETS.Rmd in epistasisGA 1.9.0.
CNVfilteR: Remove false positives of CNV calling tools by using SNV callsUpdated 2 years ago

Jose Marcos Moreno-Cabrera [email protected] and Bernat Gel [email protected]

Rendered from CNVfilteR.Rmd in CNVfilteR 1.21.0.
spaSim vignetteUpdated 2 years ago

Yuzhou Feng, Anna Trigos

Rendered from vignette.Rmd in spaSim 1.9.0.
shinyMethyl: interactive visualization of Illumina 450K methylation arraysUpdated 2 years ago

Jean-Philippe Fortin, Kasper Daniel Hansen

Rendered from shinyMethyl.Rmd in shinyMethyl 1.43.0.
SEtoolsUpdated 2 years ago

Pierre-Luc Germain

Rendered from SEtools.Rmd in SEtools 1.21.0.
Human Protein Atlas in RUpdated 2 years ago

Laurent Gatto

Rendered from hpar.Rmd in hpar 1.49.0.
RUVSeq: Remove Unwanted Variation from RNA-Seq DataUpdated 2 years ago

Davide Risso

Rendered from RUVSeq.Rmd in RUVSeq 1.41.0.
Introduction to the SpatialExperiment classUpdated 2 years ago

Dario Righelli, Helena L. Crowell, Lukas M. Weber

Rendered from SpatialExperiment.Rmd in SpatialExperiment 1.17.0.
ClassifyR Developer's GuideUpdated 2 years ago

Dario Strbenac, Ellis Patrick The University of Sydney, Australia.

Rendered from DevelopersGuide.Rmd in ClassifyR 3.11.0.
Introduction to TPP2D for 2D-TPP analysisUpdated 2 years ago

Nils Kurzawa

Rendered from TPP2D.Rmd in TPP2D 1.23.0.
The OGRE user guideUpdated 2 years ago

Sven Berres

Rendered from OGRE.Rmd in OGRE 1.11.0.
Linking information between FHIR resourcesUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from D_linking.Rmd in BiocFHIR 1.9.0.
Genome-wide identification and classification of transcription factors in plant genomesUpdated 2 years ago

Fabricio Almeida-Silva, Yves Van de Peer

Rendered from vignette_planttfhunter.Rmd in planttfhunter 1.7.0.
Tokenizing Text of Gene Set Enrichment AnalysisUpdated 2 years ago

Dongmin Jung

Rendered from ttgsea.Rmd in ttgsea 1.15.0.
Generating and using Ensembl based annotation packagesUpdated 2 years ago

Johannes Rainer

Rendered from ensembldb.Rmd in ensembldb 2.31.0.
RTopper user's manualUpdated 2 years ago

Luigi Marchionni

Rendered from RTopper.Rnw in RTopper 1.53.0.
crisprVerse: ecosystem of R packages for CRISPR gRNA designUpdated 2 years ago

Jean-Philippe Fortin, Luke Hoberecht

Rendered from crisprVerse.Rmd in crisprVerse 1.9.0.
A machine learning tutorial tutorial: applications of the Bioconductor MLInterfaces package to gene expression dataUpdated 2 years ago

VJ Carey, P. Atieno

Rendered from MLprac2_2.Rmd in MLInterfaces 1.87.0.
MLInterfaces 2.0 -- a new designUpdated 2 years ago

VJ Carey, P. Atieno

Rendered from MLint_devel.Rmd in MLInterfaces 1.87.0.
Introduction to biocthisUpdated 2 years ago

Leonardo Collado-Torres

Rendered from biocthis.Rmd in biocthis 1.17.0.
Introduction to BatchtoolsParam Updated 2 years ago

Martin Morgan

Rendered from BiocParallel_BatchtoolsParam.Rnw in BiocParallel 1.41.0.
IFAAUpdated 2 years ago

Zhigang Li

Rendered from IFAA.Rmd in IFAA 1.9.0.
User tutorial of the SynergyFinder PlusUpdated 2 years ago

Shuyu Zheng, Wenyu Wang, and Jing Tang Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki

Rendered from User_tutorual_of_the_SynergyFinder_plus.Rmd in synergyfinder 3.15.0.
Biobase development and the new eSetUpdated 2 years ago

Martin T. Morgan, H. Khan

Rendered from BiobaseDevelopment.Rmd in Biobase 2.67.0.
RcisTarget: Transcription factor binding motif enrichmentUpdated 2 years ago

Gert Hulselmans

Rendered from RcisTarget_MainTutorial.Rmd in RcisTarget 1.27.0.
uncoverappLib: a R shiny package containing unCOVERApp an interactive graphical application for clinical assessment of sequence coverage at the base-pair levelUpdated 2 years ago

Emanuela Iovino , Tommaso Pippucci

Rendered from uncoverappLib.Rmd in uncoverappLib 1.17.0.
OCTAD: Open Cancer TherApeutic DiscoveryUpdated 2 years ago

E. Chekalin

Rendered from octad.Rmd in octad 1.9.0.
esApply IntroductionUpdated 2 years ago

R. Gentleman, V. Carey, M. Morgan, S. Falcon, H. Khan

Rendered from esApply.Rmd in Biobase 2.67.0.
Graph DesignUpdated 2 years ago

R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon, Halimat C. Atanda

Rendered from GraphClass.Rmd in graph 1.85.0.
Clinical trial randomization infrastructureUpdated 2 years ago

Robert Gentleman

Rendered from randPack.Rnw in randPack 1.53.0.
Analysing Long Read RNA-Seq data with bambuUpdated 2 years ago

Ying Chen, Andre Sim, Yuk Kei Wan, Jonathan Göke

Rendered from bambu.Rmd in bambu 3.9.0.
NDExR - R implementaion for NDEx server APIUpdated 2 years ago

Florian J. Auer, Zaynab Hammoud, Frank Kramer

Rendered from ndexr-vignette.Rmd in ndexr 1.29.0.
RTCGA package workflowUpdated 2 years ago

Marcin Kosinski        

Rendered from RTCGA_Workflow.Rmd in RTCGA 1.37.0.
Introduction to microSTASISUpdated 2 years ago

Pedro Sánchez Sánchez

Rendered from microSTASIS.Rmd in microSTASIS 1.7.0.
R Package for Analyzing Tomo-seq DataUpdated 2 years ago

Ryosuke Matsuzawa

Rendered from tomoseqr.Rmd in tomoseqr 1.11.0.
OpenCyto: How to use different auto gating functionsUpdated 2 years ago

Mike Jiang

Rendered from HowToAutoGating.Rmd in openCyto 2.19.0.
An Introduction to the openCyto packageUpdated 2 years ago

Mike Jiang

Rendered from openCytoVignette.Rmd in openCyto 2.19.0.
Introduction to TargetDecoyUpdated 2 years ago

Elke Debrie, Adriaan Sticker, Milan Malfait, Lieven Clement

Rendered from TargetDecoy.Rmd in TargetDecoy 1.13.0.
Benchmark Data ManipulationUpdated 2 years ago

Shian Su

Rendered from DataManipulation.Rmd in CellBench 1.23.0.
Tidyverse PatternsUpdated 2 years ago

Shian Su

Rendered from TidyversePatterns.Rmd in CellBench 1.23.0.
Quantifying similarity between copy number profilesUpdated 2 years ago

Astrid Deschênes, Pascal Belleau and Alexander Krasnitz

Rendered from CNVMetrics.Rmd in CNVMetrics 1.11.0.
Assessing synteny identificationUpdated 2 years ago

Fabricio Almeida-Silva, Yves Van de Peer

Rendered from vignette_03_assessing_synteny.Rmd in cogeqc 1.11.0.
tLOHUpdated 2 years ago

Michelle Webb

Rendered from tLOH_vignette.Rmd in tLOH 1.15.0.
NoRCE: Noncoding RNA Set Cis Annotation and EnrichmentUpdated 2 years ago

Gulden Olgun

Rendered from NoRCE.Rmd in NoRCE 1.19.0.
Introduction to crisprVizUpdated 2 years ago

Luke Hoberecht

Rendered from intro.Rmd in crisprViz 1.9.0.
crisprBwa: alignment of gRNA spacer sequences using BWAUpdated 2 years ago

Jean-Philippe Fortin

Rendered from crisprBwa.Rmd in crisprBwa 1.11.0.
crisprBowtie: alignment of gRNA spacer sequences using bowtieUpdated 2 years ago

Jean-Philippe Fortin

Rendered from crisprBowtie.Rmd in crisprBowtie 1.11.0.
MetaPhORUpdated 2 years ago

Emily Isenhart

Rendered from MetaPhOR-vignette.Rmd in MetaPhOR 1.9.0.
Gene set scores computation with NetActivityUpdated 2 years ago

Carlos Ruiz Arenas

Rendered from NetActivity.Rmd in NetActivity 1.9.0.
Handling FHIR documents with BiocFHIRUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from B_handling.Rmd in BiocFHIR 1.9.0.
BiocFHIR -- infrastructure for parsing and analyzing FHIR dataUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from BiocFHIR.Rmd in BiocFHIR 1.9.0.
OCplus IntroductionUpdated 2 years ago

Alexander Ploner

Rendered from OCplus.Rnw in OCplus 1.81.0.
Transforming FHIR documents to tables with BiocFHIRUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from C_tables.Rmd in BiocFHIR 1.9.0.
Upper level FHIR conceptsUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from A_upper.Rmd in BiocFHIR 1.9.0.
metabinRUpdated 2 years ago

Anestis Gkanogiannis

Rendered from metabinR_vignette.Rmd in metabinR 1.9.0.
Introduction to the Robust longitudinal Differential Expression (RolDE) methodUpdated 2 years ago

Medical Bioinformatics Centre

Rendered from Introduction.Rmd in RolDE 1.11.0.
Moonlight: an approach to identify multiple role of biomarkers as oncogene or tumorsuppressor in different tumor types and stages.Updated 2 years ago

Antonio Colaprico^+^ , Catharina Olsen^+^, Claudia Cava, Thilde Terkelsen, Laura Cantini, Gloria Bertoli, Andre Olsen, Andrei Zinovyev, Emmanuel Barillot, Isabella Castiglioni, Elena Papaleo, Gianluca Bontempi

Rendered from Moonlight.Rmd in MoonlightR 1.33.0.
Visualization and annotation of read signal over genomic ranges with profileplyrUpdated 2 years ago

Doug Barrows and Tom Carroll

Rendered from profileplyr.Rmd in profileplyr 1.23.0.
Analyzing Cellular DNA Barcode with CellBarcodeUpdated 2 years ago

Wenjie Sun, Anne-Marie Lyne

Rendered from UMI_VDJ_Barcode.Rmd in CellBarcode 1.13.0.
Vignette of the pengls packageUpdated 2 years ago

Stijn Hawinkel

Rendered from penglsVignette.Rmd in pengls 1.13.0.
Finding local maxima with MassSpecWaveletUpdated 2 years ago

Sergio Oller

Rendered from FindingLocalMaxima.Rmd in MassSpecWavelet 1.73.0.
PRAM: Pooling RNA-seq and Assembling ModelsUpdated 2 years ago

Peng Liu, Colin N. Dewey, and Sündüz Keleş

Rendered from pram.Rmd in pram 1.23.0.
Sincell: Analysis of cell state hierarchies from single-cell RNA-seqUpdated 2 years ago

Miguel Julia

Rendered from sincell-vignette.Rnw in sincell 1.39.0.
Illustration of MEFISTO on simulated data with a temporal covariateUpdated 2 years ago

Britta Velten

Rendered from MEFISTO_temporal.Rmd in MOFA2 1.17.0.
RCX - an R package implementing the Cytoscape Exchange (CX) format Updated 2 years ago

Florian J. Auer

Rendered from RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd in RCX 1.11.0.
FuseSOM package manualUpdated 2 years ago

Elijah Willie

Rendered from Introduction.Rmd in FuseSOM 1.9.0.
DiffBind: Differential binding analysis of ChIP-Seq peak dataUpdated 2 years ago

Rory Stark

Rendered from DiffBind.Rnw in DiffBind 3.17.0.
Computation of melting temperature of nucleic acid duplexes with rmeltingUpdated 2 years ago

Aravind, J.^1^ and Krishna, G. K.^2^

Rendered from Tutorial.Rmd in rmelting 1.23.0.
scds:single cell doublet scoring: In-silico doublet annotation for single cell RNA sequencing dataUpdated 2 years ago

Dennis Kostka

Rendered from scds.Rmd in scds 1.23.0.
CalculatingrfPredscoreswithpackagerfPredUpdated 2 years ago

Hugo Varet

Rendered from vignette.Rnw in rfPred 1.45.0.
Robust Probabilistic Averaging (RPA)Updated 2 years ago

Leo Lahti

Rendered from RPA.Rmd in RPA 1.63.0.
Proteolytic resistance analysisUpdated 2 years ago

Valentina Cappelletti ([email protected]), Malinovska Liliana ([email protected]), Devon Kohler ([email protected])

Rendered from Proteolytic_resistance_notebook.Rmd in MSstatsLiP 1.13.0.
MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP packageUpdated 2 years ago

Devon Kohler ([email protected])

Rendered from MSstatsLiP_Workflow.Rmd in MSstatsLiP 1.13.0.
Example dataset with ConfounderingUpdated 2 years ago

Jakob Wirbel and Georg Zeller

Rendered from SIAMCAT_confounder.Rmd in SIAMCAT 2.11.0.
Holdout Testing with SIAMCATUpdated 2 years ago

Jakob Wirbel, Konrad Zych, and Georg Zeller

Rendered from SIAMCAT_holdout.Rmd in SIAMCAT 2.11.0.
Meta-analysis using SIAMCATUpdated 2 years ago

Jakob Wirbel, and Georg Zeller

Rendered from SIAMCAT_meta.Rmd in SIAMCAT 2.11.0.
Machine learning pitfallsUpdated 2 years ago

Jakob Wirbel and Georg Zeller

Rendered from SIAMCAT_ml_pitfalls.Rmd in SIAMCAT 2.11.0.
Fragment matching using synapterUpdated 2 years ago

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered from fragmentmatching.Rmd in synapter 2.31.0.
| Nested Effects Models-based perturbation inference: | Inference of unobserved perturbations from gene expression profiles.Updated 2 years ago

Martin Pirkl, Niko Beerenwinkel

Rendered from nempi.Rmd in nempi 1.15.0.
An introduction to biodbUniprotUpdated 2 years ago

Pierrick Roger

Rendered from biodbUniprot.Rmd in biodbUniprot 1.13.0.
Structure and content of RAVmodelUpdated 2 years ago

Sehyun Oh

Rendered from Contents.Rmd in GenomicSuperSignature 1.15.0.
Mining high-confidence candidate genes with cageminerUpdated 2 years ago

Fabricio Almeida-Silva, Thiago Motta Venancio

Rendered from cageminer.Rmd in cageminer 1.13.0.
famatUpdated 2 years ago

Emilie Secherre

Rendered from famat.Rmd in famat 1.17.0.
Spiky: Analysing cfMeDIP-seq data with spike-in controlsUpdated 2 years ago

Samantha L Wilson and Lauren M Harmon

Rendered from spiky_vignette.Rmd in spiky 1.13.0.
xcore vignetteUpdated 2 years ago

migdal

Rendered from xcore_vignette.Rmd in xcore 1.11.0.
Introduction to iSEEhubUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from iSEEhub.Rmd in iSEEhub 1.9.0.
An Introduction to FastqCleanerUpdated 2 years ago

Leandro Roser, Fernán Agüero, Daniel Sánchez

Rendered from Overview.Rmd in FastqCleaner 1.25.0.
Demultiplexing oligonucleotide-labeled scRNA-seq data with demuxmixUpdated 2 years ago

Hans-Ulrich Klein

Rendered from demuxmix.Rmd in demuxmix 1.9.0.
Obtain and Display H3K27ac K562 track from the AnnotationHubUpdated 2 years ago

Paul Shannon

Rendered from v06.annotationHub.Rmd in igvR 1.27.0.
Clone ID with cardelinoUpdated 2 years ago

Davis McCarthy, Yuanhua Huang

Rendered from vignette-cloneid.Rmd in cardelino 1.9.0.
The ChIPanalyser User's GuideUpdated 2 years ago

Patrick Martin

Rendered from ChIPanalyser.Rmd in ChIPanalyser 1.29.0.
The ChIPanalyser User's GuideUpdated 2 years ago

Patrick Martin

Rendered from GA_ChIPanalyser.Rmd in ChIPanalyser 1.29.0.
Herper Quick Start GuideUpdated 2 years ago

Matt Paul - [email protected]

Rendered from QuickStart.Rmd in Herper 1.17.0.
In-silico cleavage of polypeptides using the cleaver packageUpdated 2 years ago

Sebastian Gibb

Rendered from cleaver.Rmd in cleaver 1.45.0.
phenomis: Postprocessing and univariate statistical analysis of omics dataUpdated 2 years ago

Etienne A. Thevenot

Rendered from phenomis-vignette.Rmd in phenomis 1.9.0.
regioneReloadedUpdated 2 years ago

Roberto Malinverni

Rendered from regioneReloaded.Rmd in regioneReloaded 1.9.0.
Introduction to magreneUpdated 2 years ago

Fabricio Almeida-Silva, Yves Van de Peer

Rendered from magrene.Rmd in magrene 1.9.0.
Advanced usage of onlineFDRUpdated 2 years ago

David S. Robertson

Rendered from advanced-usage.Rmd in onlineFDR 2.15.0.
The theory behind onlineFDRUpdated 2 years ago

David S. Robertson

Rendered from theory.Rmd in onlineFDR 2.15.0.
Managing online multiple hypothesis testing using the onlineFDR packageUpdated 2 years ago

David S. Robertson, Lathan Liou, Aaditya Ramdas and Natasha A. Karp

Rendered from onlineFDR.Rmd in onlineFDR 2.15.0.
BiocBaseUtils Quick StartUpdated 2 years ago

Bioconductor Core Team

Rendered from BiocBaseUtils.Rmd in BiocBaseUtils 1.9.0.
miRNA and pathway analysis with PanomiRUpdated 2 years ago

Pourya Naderi, Alan Teo, Ilya Sytchev, and Winston Hide

Rendered from PanomiR.Rmd in PanomiR 1.11.0.
metabomxtrUpdated 2 years ago

Michael Nodzenski

Rendered from Metabomxtr_Vignette.Rnw in metabomxtr 1.41.0.
mixnormUpdated 2 years ago

Michael Nodzenski

Rendered from mixnorm_Vignette.Rnw in metabomxtr 1.41.0.
FGGA: Factor Graph GO AnnotationUpdated 2 years ago

F.E. Spetale, E. Tapia

Rendered from fgga.Rmd in fgga 1.15.0.
Contributing to iSEEhubUpdated 2 years ago

Kevin Rue-Albrecht

Rendered from contributing.Rmd in iSEEhub 1.9.0.
Analyses of high-throughput data from heterogeneous samples with TOASTUpdated 2 years ago

Ziyi Li, Hao Wu

Rendered from TOAST.Rmd in TOAST 1.21.0.
Case StudiesUpdated 2 years ago

Tiago Chedraoui Silva

Rendered from casestudy.Rmd in TCGAbiolinks 2.35.0.
Utilizing Mechanism-Aware Imputation (MAI)Updated 2 years ago

Jonathan Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh, Katerina Kechris

Rendered from UsingMAI.Rmd in MAI 1.13.0.
gwascat: structuring and querying the NHGRI GWAS catalogUpdated 2 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from gwascat.Rmd in gwascat 2.39.0.
NuPoP: Nucleosomes Positioning PredictionUpdated 2 years ago

Ji-Ping Wang, Liqun Xi and Oscar Zarate

Rendered from NuPoP.Rmd in NuPoP 2.15.0.
TFHAZUpdated 2 years ago

Alberto Marchesi [email protected], Marco Masseroli

Rendered from TFHAZ.Rmd in TFHAZ 1.29.0.
Introduction to plotgardenerUpdated 2 years ago

Nicole Kramer, Eric S. Davis, Craig Wenger, Sarah Parker, Erika Deoudes, Michael Love, Douglas H. Phanstiel

Rendered from introduction_to_plotgardener.Rmd in plotgardener 1.13.0.
An introduction to BASiCStanUpdated 2 years ago

Alan O'Callaghan

Rendered from BASiCStan.Rmd in BASiCStan 1.9.0.
HOWTO generate biocViews HTMLUpdated 2 years ago

S. Falcon and V.J. Carey

Rendered from HOWTO-BCV.Rmd in biocViews 1.75.0.
HOWTO generate repository HTMLUpdated 2 years ago

S. Falcon

Rendered from createReposHtml.Rmd in biocViews 1.75.0.
The DSS User's GuideUpdated 2 years ago

Hao Wu, [email protected]

Rendered from DSS.Rmd in DSS 2.55.0.
Random Numbers in BiocParallelUpdated 2 years ago

Martin Morgan

Rendered from Random_Numbers.Rmd in BiocParallel 1.41.0.
GWAS TracksUpdated 2 years ago

Paul Shannon

Rendered from v07.gwas.Rmd in igvR 1.27.0.
FstUpdated 2 years ago

David Clayton

Rendered from Fst-vignette.Rnw in snpStats 1.57.0.
GenomicSuperSignature - QuickstartUpdated 2 years ago

Sehyun Oh

Rendered from Quickstart.Rmd in GenomicSuperSignature 1.15.0.
Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylationUpdated 2 years ago

Paul Shannon

Rendered from v03.ctcfChIP.Rmd in igvR 1.27.0.
Introduction: a simple demoUpdated 2 years ago

Paul Shannon

Rendered from v00.basicIntro.Rmd in igvR 1.27.0.
Paired-end Interaction TracksUpdated 2 years ago

Paul Shannon

Rendered from v04.pairedEnd.Rmd in igvR 1.27.0.
Use a Custom GenomeUpdated 2 years ago

Paul Shannon

Rendered from v02.customGenome.Rmd in igvR 1.27.0.
Use a Stock GenomeUpdated 2 years ago

Paul Shannon

Rendered from v01.stockGenome.Rmd in igvR 1.27.0.
Example workflow for processing of raw spectral cytometry filesUpdated 2 years ago

Jakob Theorell

Rendered from flowSpecs_vinjette.Rmd in flowSpecs 1.21.0.
packFinderUpdated 2 years ago

Jack Gisby

Rendered from packFinder.Rmd in packFinder 1.19.0.
Introduction to densvisUpdated 2 years ago

Alan O'Callaghan

Rendered from densvis.Rmd in densvis 1.17.0.
Rcpi: R/Bioconductor Package as an Integrated Informatics Platform for Drug DiscoveryUpdated 2 years ago

Nan Xiao <https://nanx.me>

Rendered from Rcpi.Rmd in Rcpi 1.43.0.
New Implementation of the HIBAG Algorithm with Latest Intel IntrinsicsUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from Implementation.Rmd in HIBAG 1.43.1.
HIBAG -- an R Package for HLA Genotype Imputation with Attribute BaggingUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from HIBAG.Rmd in HIBAG 1.43.1.
HIBAG -- an R Package for HLA Genotype Imputation with Attribute BaggingUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from HLA_Association.Rmd in HIBAG 1.43.1.
Integration with RUpdated 2 years ago

Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered from SeqArray.Rmd in SeqArray 1.47.0.
SeqArray Data Format and AccessUpdated 2 years ago

Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered from SeqArrayTutorial.Rmd in SeqArray 1.47.0.
SeqArray OverviewUpdated 2 years ago

Dr. Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered from OverviewSlides.Rmd in SeqArray 1.47.0.
R Interface to CoreArray Genomic Data Structure (GDS) FilesUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from gdsfmt.Rmd in gdsfmt 1.43.0.
Tutorials for the R/Bioconductor Package SNPRelateUpdated 2 years ago

Xiuwen Zheng (Department of Biostatistics, University of Washington -- Seattle)

Rendered from SNPRelate.Rmd in SNPRelate 1.41.0.
Case study: command-line interface (CLI) tutorialUpdated 2 years ago

Nuno Saraiva-Agostinho

Rendered from CLI_tutorial.Rmd in psichomics 1.33.0.
satuRn - vignetteUpdated 2 years ago

Jeroen Gilis

Rendered from Vignette.Rmd in satuRn 1.15.0.
Chronological and gestational DNAm age estimation using different methylation-based clocksUpdated 2 years ago

Institute for Global Health (ISGlobal), Barcelona, Spain Bioinformatics Research Group in Epidemiolgy (BRGE) http://brge.isglobal.org

Rendered from methylclock.Rmd in methylclock 1.13.0.
Applying CTSV to Spatial Transcriptomics DataUpdated 2 years ago

Jinge Yu, Xiangyu Luo

Rendered from CTSV.Rmd in CTSV 1.9.0.
Introduction to the CHETAH packageUpdated 2 years ago

Jurrian de Kanter

Rendered from CHETAH_introduction.Rmd in CHETAH 1.23.0.
ggtreeExtraUpdated 2 years ago

| Shuangbin Xu and GuangChuang Yu | School of Basic Medical Sciences, Southern Medical University

Rendered from ggtreeExtra.Rmd in ggtreeExtra 1.17.0.
Cogito: Compare annotated genomic intervals toolUpdated 2 years ago

Annika Buerger

Rendered from Cogito.Rmd in Cogito 1.13.0.
Using factRUpdated 2 years ago

Fursham Hamid

Rendered from factR.Rmd in factR 1.9.0.
EasyCellType: an example workflowUpdated 2 years ago

Ruoxing Li

Rendered from my-vignette.Rmd in EasyCellType 1.9.0.
Estimating Enrichment in PhIP-Seq Experiments with BEERUpdated 2 years ago

Athena Chen, Kai Kammers, Rob Scharpf, Ingo Ruczinski

Rendered from beer.Rmd in beer 1.11.0.
Handling metadata and annotationsUpdated 2 years ago

AlpsNMR authors

Rendered from Vig02-handling-metadata-and-annotations.Rmd in AlpsNMR 4.9.0.
CoreGx: Class and Function Abstractions for PharmacoGx, RadioGx and ToxicoGxUpdated 2 years ago

Petr Smirnov, Ian Smith, Christopher Eeles, Benjamin Haibe-Kains

Rendered from coreGx.Rmd in CoreGx 2.11.0.
The TreatmentResponseExperiment ClassUpdated 2 years ago

Petr Smirnov, Christopher Eeles

Rendered from TreatmentResponseExperiment.Rmd in CoreGx 2.11.0.
ATACseqTFEA GuideUpdated 2 years ago

Jianhong Ou

Rendered from ATACseqTFEA.Rmd in ATACseqTFEA 1.9.0.
Getting started with rprimerUpdated 2 years ago

Sofia Persson

Rendered from getting-started-with-rprimer.Rmd in rprimer 1.11.0.
QC and downstream analysis for differential expression RNA-seqUpdated 2 years ago

Lorena Pantano

Rendered from DEGreport.Rmd in DEGreport 1.43.0.
Docker/Singularity ContainersUpdated 2 years ago

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered from docker.Rmd in EpiCompare 1.11.0.
RedisParam for DevelopersUpdated 2 years ago

Jiefei Wang

Rendered from RedisParamDeveloperGuide.Rmd in RedisParam 1.9.0.
Using RedisParamUpdated 2 years ago

Martin Morgan

Rendered from RedisParamUserGuide.Rmd in RedisParam 1.9.0.
METAbolic pathway testing combining POsitive and NEgative mode data (metapone)Updated 2 years ago

Tianwei Yu

Rendered from metapone.Rmd in metapone 1.13.0.
DegNorm: an R package for degradation normalization for RNA-seq dataUpdated 2 years ago

Bin Xiong, Ji-Ping Wang

Rendered from DegNorm.Rmd in DegNorm 1.17.0.
EnMCBUpdated 2 years ago

Xin Yu

Rendered from vignette.Rmd in EnMCB 1.19.0.
Normalization by distributional resampling of high throughput single-cell RNA-sequencing dataUpdated 2 years ago

Jared Brown and Christina Kendziorski

Rendered from Dino.Rmd in Dino 1.13.0.
scMET Bayesian modelling of DNA methylation heterogeneity at single-cell resolutionUpdated 2 years ago

Andreas C. Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina Vallejos

Rendered from scMET_vignette.Rmd in scMET 1.9.0.
scDDboostUpdated 2 years ago

Xiuyu Ma

Rendered from scDDboost.Rmd in scDDboost 1.9.0.
CexoR VignetteUpdated 2 years ago

Pedro Madrigal

Rendered from CexoR.Rnw in CexoR 1.45.0.
RgnTX: colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguityUpdated 2 years ago

Yue Wang, Jia Meng

Rendered from RgnTX.Rmd in RgnTX 1.9.0.
eds: Low-level reader function for Alevin EDS formatUpdated 2 years ago

Avi Srivastava

Rendered from eds.Rmd in eds 1.9.0.
Introduction to MfuzzUpdated 3 years ago

Matthias Futschik

Rendered from Mfuzz.Rnw in Mfuzz 2.67.0.
BOBaFITUpdated 3 years ago

Gaia Mazzocchetti

Rendered from BOBaFIT.Rmd in BOBaFIT 1.11.0.
Data preparation using TCGA-BRCA databaseUpdated 3 years ago

Gaia Mazzocchetti

Rendered from Data-Preparation.Rmd in BOBaFIT 1.11.0.
orthogene: Getting StartedUpdated 3 years ago

Author: Brian M. Schilder

Rendered from orthogene.Rmd in orthogene 1.13.0.
Package Quick Start GuideUpdated 3 years ago

Jiefei Wang

Rendered from quick_start_guide.Rmd in SharedObject 1.21.0.
MultiAssayExperiment: Quick Start GuideUpdated 3 years ago

Marcel Ramos & Levi Waldron

Rendered from QuickStartMultiAssay.Rmd in MultiAssayExperiment 1.33.1.
MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry dataUpdated 3 years ago

Thomas Naake

Rendered from MetNet.Rmd in MetNet 1.25.0.
Stemness scoreUpdated 3 years ago

Tiago Chedraoui Silva

Rendered from stemness_score.Rmd in TCGAbiolinks 2.35.0.
singscoreUpdated 3 years ago

Ruqian Lyu

Rendered from singscore.Rmd in singscore 1.27.0.
Using the GEOquery PackageUpdated 3 years ago

Sean Davis

Rendered from GEOquery.Rmd in GEOquery 2.75.0.
SUITOR: selecting the number of mutational signaturesUpdated 3 years ago

DongHyuk Lee and Bin Zhu

Rendered from vignette.Rmd in SUITOR 1.9.0.
FindIT2:Find influential TF and influential TargetUpdated 3 years ago

Guandong Shang

Rendered from FindIT2.Rmd in FindIT2 1.13.0.
Analyzing Hi-C and HiChIP data with HiCDCPlusUpdated 3 years ago

Merve Sahin

Rendered from HiCDCPlus.Rmd in HiCDCPlus 1.15.0.
Introduction to OLINUpdated 3 years ago

Matthias Futschik

Rendered from OLIN.Rnw in OLIN 1.85.0.
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltrUpdated 3 years ago

Pooja Gangras

Rendered from surfaltr_vignette.Rmd in surfaltr 1.13.0.
spongeEffects.RmdUpdated 3 years ago

Hoffmann M - Boniolo F

Rendered from spongEffects.Rmd in SPONGE 1.29.0.
Rcpi Quick Reference CardUpdated 3 years ago

Nan Xiao <https://nanx.me>

Rendered from Rcpi-quickref.Rmd in Rcpi 1.43.0.
canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCCUpdated 3 years ago

Karim Mezhoud

Rendered from canceR.Rmd in canceR 1.41.0.
pRolocGUI - Interactive visualisation of spatial proteomics dataUpdated 3 years ago

Lisa Breckels, Thomas Naake, Laurent Gatto

Rendered from pRolocGUI.Rmd in pRolocGUI 2.17.0.
RAREsim VignetteUpdated 3 years ago

Ryan Barnard

Rendered from RAREsim_Vignette.Rmd in RAREsim 1.11.0.
ToxicoGx: An R Platform for Integrated Toxicogenomics Data AnalysisUpdated 3 years ago

Sisira Kadambat Nair, Esther Yoo, Christopher Eeles, Amy Tang, Nehme El-Hachem, Petr Smirnov, Benjamin Haibe-Kains

Rendered from toxicoGxCaseStudies.Rmd in ToxicoGx 2.11.0.
Introduction to the microbiome R packageUpdated 3 years ago

Leo Lahti, Sudarshan Shetty, et al.

Rendered from vignette.Rmd in microbiome 1.29.0.
Introduction to BAnOCC (Bayesian Analaysis Of Compositional Covariance)Updated 3 years ago

Emma Schwager

Rendered from banocc-vignette.Rmd in banocc 1.31.0.
PROGENy pathway signaturesUpdated 3 years ago

Pau Badia-i-Mompel

Rendered from progeny.Rmd in progeny 1.29.0.
Using fmrs packageUpdated 3 years ago

Farhad Shokoohi

Rendered from usingfmrs.Rmd in fmrs 1.17.0.
coMET users guideUpdated 3 years ago

Tiphaine Martin

Rendered from coMET.Rnw in coMET 1.39.0.
MS2 chromatograms based alignment of targeted mass-spectrometry runsUpdated 3 years ago

Shubham Gupta and Hannes Röst

Rendered from DIAlignR-vignette.Rmd in DIAlignR 2.15.0.
motifStack VignetteUpdated 3 years ago

Jianhong Ou, Michael Brodsky, Lihua Julie Zhu

Rendered from motifStack_HTML.Rmd in motifStack 1.51.0.
Sparse Partial correlation ON Gene Expression with SPONGEUpdated 3 years ago

Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz

Rendered from SPONGE.Rmd in SPONGE 1.29.0.
Workflow_WTAUpdated 3 years ago

Nicole Ortogero

Rendered from Workflow_WTA_kidney.Rmd in GeoDiff 1.13.0.
Decontamination of ambient RNA in single-cell genomic data with DecontXUpdated 3 years ago

Shiyi (Iris) Yang, Zhe Wang, Yuan Yin, Joshua Campbell

Rendered from decontX.Rmd in celda 1.23.0.
GenomicInteractionNodes GuideUpdated 3 years ago

Jianhong Ou, Yu Xiang, Xiaolin Wei, and Yarui Diao

Rendered from GenomicInteractionNodes_vignettes.Rmd in GenomicInteractionNodes 1.11.0.
Developer Introduction to the NanoStringGeoMxSetUpdated 3 years ago

David Henderson, Patrick Aboyoun, Nicole Ortogero, Zhi Yang, Jason Reeves, Kara Gorman, Rona Vitancol, Thomas Smith, Maddy Griswold

Rendered from Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd in GeomxTools 3.11.0.
FGNetUpdated 3 years ago

Sara Aibar

Rendered from FGNet.Rmd in FGNet 3.41.0.
mirTarRnaSeqUpdated 3 years ago

Mercedeh Movassagh

Rendered from mirTarRnaSeq.Rmd in mirTarRnaSeq 1.15.0.
2 - Introduction: Input dataUpdated 3 years ago

Tiago Chedraoui Silva

Rendered from input.Rmd in ELMER 2.31.0.
Use DepInfeR package to infer sample-specific protein dependencies from drug-protein profiling and ex-vivo drug response dataUpdated 3 years ago

Alina Batzilla, Junyan Lu

Rendered from vignette.Rmd in DepInfeR 1.11.0.
Motif enrichment with backgroundUpdated 3 years ago

Gert Hulselmans

Rendered from Tutorial_AnalysisWithBackground.Rmd in RcisTarget 1.27.0.
SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypesUpdated 3 years ago

Konrad Zych, Jakob Wirbel, and Georg Zeller

Rendered from SIAMCAT_vignette.Rmd in SIAMCAT 2.11.0.
Details on biodbUpdated 3 years ago

Pierrick Roger

Rendered from details.Rmd in biodb 1.15.0.
An introduction to biodbUpdated 3 years ago

Pierrick Roger

Rendered from biodb.Rmd in biodb 1.15.0.
Example usage of seqArchR on simulated DNA sequencesUpdated 3 years ago

Sarvesh Nikumbh

Rendered from seqArchR.Rmd in seqArchR 1.11.0.
ASURATUpdated 3 years ago

Keita Iida

Rendered from ASURAT.Rmd in ASURAT 1.11.0.
IntroductionUpdated 3 years ago

Tiago Chedraoui Silva

Rendered from index.Rmd in TCGAbiolinks 2.35.0.
How to visualize complex heatmaps interactivelyUpdated 3 years ago

Zuguang Gu ( [email protected] )

Rendered from InteractiveComplexHeatmap.Rmd in InteractiveComplexHeatmap 1.15.0.
IntroductionUpdated 3 years ago

Pau Badia-i-Mompel, Jesús Vélez-Santiago

Rendered from decoupleR.Rmd in decoupleR 2.13.0.
InPAS VignetteUpdated 3 years ago

Jianhong Ou, Haibo Liu, Sungmi Park, Michael Green, Lihua Julie Zhu

Rendered from InPAS.Rmd in InPAS 2.15.0.
Introduction to coMethDMRUpdated 3 years ago

Lissette Gomez, Gabriel Odom, Tiago Chedraoui Silva, Lanyu Zhang, and Lily Wang

Rendered from vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd in coMethDMR 1.11.0.
BiRewireUpdated 3 years ago

Andrea Gobbi

Rendered from BiRewire.Rnw in BiRewire 3.39.0.
FlowSOMUpdated 3 years ago

Sofie Van Gassen

Rendered from FlowSOM.Rnw in FlowSOM 2.15.0.
Advanced Screen Analysis: Contrast ComparisonsUpdated 3 years ago

Russell Bainer

Rendered from Contrast_Comparisons.Rmd in gCrisprTools 2.13.0.
Example Workflow For Processing a Single Pooled ScreenUpdated 3 years ago

Russell Bainer

Rendered from Crispr_example_workflow.Rmd in gCrisprTools 2.13.0.
CBEA: Competitive Balances for Taxonomic Enrichment AnalysisUpdated 3 years ago

Quang P.Nguyen, Anne G. Hoen, H. Robert Frost

Rendered from basic_usage.Rmd in CBEA 1.7.0.
Using rgoslin to parse and normalize lipid nomenclatureUpdated 3 years ago

Nils Hoffmann

Rendered from introduction.Rmd in rgoslin 1.11.0.
An introduction to biodbNcbiUpdated 3 years ago

Pierrick Roger

Rendered from biodbNcbi.Rmd in biodbNcbi 1.11.0.
An Introduction to the rgsepd packageUpdated 3 years ago

Karl Stamm

Rendered from rgsepd.Rnw in rgsepd 1.39.0.
An introduction to RbwaUpdated 3 years ago

Jean-Philippe Fortin

Rendered from Rbwa.Rmd in Rbwa 1.11.0.
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data with CellNOptRUpdated 3 years ago

Camille Terfve, Thomas Cokelaer, Aidan MacNamara, Enio Gjerga, Attila Gabor, Panuwat Trairatphisan, Julio Saez-Rodriguez

Rendered from CellNOptR-vignette.Rmd in CellNOptR 1.53.0.
An introduction to biodbNciUpdated 3 years ago

Pierrick Roger

Rendered from biodbNci.Rmd in biodbNci 1.11.0.
Introduction to MFAUpdated 3 years ago

Kieran R Campbell

Rendered from introduction_to_mfa.Rmd in mfa 1.29.0.
Working with PSM dataUpdated 3 years ago

Laurent Gatto

Rendered from PSM.Rmd in PSMatch 1.11.0.
Intro_to_Marker_Enrichment_Modeling_AnalysisUpdated 3 years ago

Kirsten Diggins, Sierra Lima, Jonathan Irish

Rendered from Intro_to_Marker_Enrichment_Modeling_Analysis.Rmd in cytoMEM 1.11.0.
vissE: Visualising Set Enrichment Analysis Results.Updated 3 years ago

Dharmesh D. Bhuva

Rendered from vissE.Rmd in vissE 1.15.0.
An introduction to biodbChebiUpdated 3 years ago

Pierrick Roger

Rendered from biodbChebi.Rmd in biodbChebi 1.13.0.
Robust Model-based Clustering of Flow Cytometry Data The flowClust packageUpdated 3 years ago

Raphael Gottardo, Kenneth Lo and Greg Finak

Rendered from flowClust.Rmd in flowClust 3.45.0.
CIMICE-R: (Markov) Chain Method to Infer Cancer EvolutionUpdated 3 years ago

Nicolò Rossi

Rendered from CIMICER.Rmd in CIMICE 1.15.0.
kissDE Reference ManualUpdated 3 years ago

Aurélie Siberchicot

Rendered from kissDE.rnw in kissDE 1.27.0.
RMassBank: Non-standard usageUpdated 3 years ago

Michael Stravs

Rendered from RMassBankNonstandard.Rmd in RMassBank 3.17.0.
Contextualizing large scale signalling networks from expression footprints with CARNIVALUpdated 3 years ago

Enio Gjerga, Matteo Spatuzzi, Olga Ivanova,

Rendered from CARNIVAL.Rmd in CARNIVAL 2.17.0.
RMassBank: The workflow by exampleUpdated 3 years ago

Michael Stravs, Emma Schymanski

Rendered from RMassBank.Rmd in RMassBank 3.17.0.
ILoReg package manualUpdated 3 years ago

Johannes Smolander

Rendered from ILoReg.Rmd in ILoReg 1.17.0.
Determine population ancestry from DNAm arraysUpdated 3 years ago

Sean K. Maden

Rendered from recountmethylation_glint.Rmd in recountmethylation 1.17.0.
Power analysis for DNAm arraysUpdated 3 years ago

Sean K. Maden

Rendered from recountmethylation_pwrewas.Rmd in recountmethylation 1.17.0.
Interactive and explorative visualization of ExpressionSet using omicsViewerUpdated 3 years ago

Chen Meng

Rendered from quickStart.rmd in omicsViewer 1.11.0.
APAlyzer: A toolkit for APA analysis using RNA-seq dataUpdated 3 years ago

Ruijia Wang, Bin Tian

Rendered from APAlyzer.Rmd in APAlyzer 1.21.0.
Data analysis of metabolomics and other omics datasets using the structToolboxUpdated 3 years ago

Gavin R Lloyd, Andris Jankevics, Ralf J Weber

Rendered from data_analysis_omics_using_the_structtoolbox.Rmd in structToolbox 1.19.0.
sarks-vignetteUpdated 3 years ago

Dennis Wylie

Rendered from sarks-vignette.Rnw in sarks 1.19.0.
MBECS introductionUpdated 3 years ago

Michael Olbrich

Rendered from mbecs_vignette.Rmd in MBECS 1.11.0.
Pathway Integrated Regression-based Kernel Association Test (PaIRKAT)Updated 3 years ago

Charlie Carpenter, Weiming Zhang, Lucas Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russel Bowler, Katerina Kechris, Debashis Ghosh

Rendered from using-pairkat.Rmd in pairkat 1.13.0.
Docker/Singularity ContainersUpdated 3 years ago

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered from docker.Rmd in orthogene 1.13.0.
MSstatsTMT : A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingUpdated 3 years ago

Ting Huang ([email protected]), Meena Choi ([email protected]), Mateusz Staniak ([email protected]), Sicheng Hao ([email protected]), Olga Vitek([email protected])

Rendered from MSstatsTMT.Rmd in MSstatsTMT 2.15.1.
Core Utils for Mass Spectrometry DataUpdated 3 years ago

MsCoreUtils Package Maintainers

Rendered from MsCoreUtils.Rmd in MsCoreUtils 1.19.0.
flowCut: Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence AnalysisUpdated 3 years ago

Justin Meskas, Sherrie Wang

Rendered from flowCut.Rmd in flowCut 1.17.0.
Creating a new connector.Updated 3 years ago

Pierrick Roger

Rendered from new_connector.Rmd in biodb 1.15.0.
MS2 fragment ionsUpdated 3 years ago

Laurent Gatto

Rendered from Fragments.Rmd in PSMatch 1.11.0.
'Motif2Site': an R package to detect binding sites from ChIP-seq and recenter themUpdated 3 years ago

Peyman Zarrineh

Rendered from Motif2Site.Rmd in Motif2Site 1.11.0.
svaNUMT Quick OverviewUpdated 3 years ago

Ruining Dong

Rendered from svaNUMT.Rmd in svaNUMT 1.13.0.
RnaSeqSampleSize: Sample size estimation by real dataUpdated 3 years ago

Shilin Zhao Developer

Rendered from RnaSeqSampleSize.Rnw in RnaSeqSampleSize 2.17.0.
tricycle: Transferable Representation and Inference of Cell CycleUpdated 3 years ago

Shijie C. Zheng

Rendered from tricycle.Rmd in tricycle 1.15.0.
Isotope pattern validation with CAMERAUpdated 3 years ago

Steffen Neumann

Rendered from IsotopeDetectionVignette.Rnw in CAMERA 1.63.0.
Molecule Identification with CAMERAUpdated 3 years ago

Steffen Neumann

Rendered from CAMERA.Rnw in CAMERA 1.63.0.
LinTInd - tutorialUpdated 3 years ago

Luyue Wang

Rendered from tutorial.Rmd in LinTInd 1.11.0.
PhIPData: A Container for PhIP-Seq ExperimentsUpdated 3 years ago

Athena Chen, Rob Scharpf, and Ingo Ruczinski

Rendered from PhIPData.Rmd in PhIPData 1.15.0.
TFEA.ChIP: a tool kit for transcription factor enrichment analysis capitalizing on ChIP-seq datasetsUpdated 3 years ago

Laura Puente-Santamaria, Luis del Peso

Rendered from TFEA.ChIP.Rmd in TFEA.ChIP 1.27.0.
YY1 ChIA-PET motif analysis (single call)Updated 3 years ago

Jennifer Hammelman, Konstantin Krismer

Rendered from single-call.Rmd in spatzie 1.13.0.
YY1 ChIA-PET motif analysis (step-by-step)Updated 3 years ago

Jennifer Hammelman, Konstantin Krismer

Rendered from individual-steps.Rmd in spatzie 1.13.0.
User guide to the dearseq R packageUpdated 3 years ago

Marine Gauthier, Denis Agniel, Boris Hejblum

Rendered from dearseqUserguide.Rmd in dearseq 1.19.0.
customCMPdb: Integrating Community and Custom Compound CollectionsUpdated 3 years ago

Authors: Yuzhu Duan, Dan Evans, Kevin Horan, Austin Leong, Siddharth Sai and Thomas Girke

Rendered from customCMPdb.Rmd in customCMPdb 1.17.0.
Use cases for coordinate mapping with ensembldbUpdated 3 years ago

Johannes Rainer, Laurent Gatto and Christian X. Weichenberger

Rendered from coordinate-mapping-use-cases.Rmd in ensembldb 2.31.0.
Reproduce the Diffusion Map vignette with the supplied data()Updated 3 years ago

Philipp Angerer

Rendered from Diffusion-Map-recap.Rmd in destiny 3.21.0.
Getting started with GenomicDistributionsUpdated 3 years ago

Nathan Sheffield

Rendered from intro.Rmd in GenomicDistributions 1.15.0.
Genome-wide methylation analysis using coMethDMR via parallel computingUpdated 3 years ago

Gabriel J. Odom, Lissette Gomez, Tiago Chedraoui Silva, Lanyu Zhang and Lily Wang

Rendered from vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd in coMethDMR 1.11.0.
ASEBUpdated 3 years ago

Likun Wang

Rendered from ASEB.Rnw in ASEB 1.51.0.
monaLisa - MOtif aNAlysis with LisaUpdated 3 years ago

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered from monaLisa.Rmd in monaLisa 1.13.0.
Regression Based Approach for Motif SelectionUpdated 3 years ago

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered from selecting_motifs_with_randLassoStabSel.Rmd in monaLisa 1.13.0.
Including inter-species measurements in differential expression analysis of RNAseq data with the compcodeR packageUpdated 3 years ago

Paul Bastide & Mélina Gallopin

Rendered from phylocompcodeR.Rmd in compcodeR 1.43.0.
Use sitePath to find fixation and parallel sitesUpdated 3 years ago

Chengyang Ji

Rendered from sitePath.Rmd in sitePath 1.23.0.
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing dataUpdated 3 years ago

Zijian Ni and Christina Kendziorski

Rendered from scCB2.Rmd in scCB2 1.17.0.
Suppl. Ch. 2 - Import and Tidy DataUpdated 3 years ago

Gabriel Odom

Rendered from Supplement2-Importing_Data.Rmd in pathwayPCA 1.23.0.
Example workflowUpdated 3 years ago

Tim Daniel Rose

Rendered from example-workflow.Rmd in mosbi 1.13.0.
tanggle: Visualización de redes filogenéticas con ggplot2Updated 3 years ago

Klaus Schliep, Marta Vidal-García, Leann Biancani, Francisco Henao-Diaz, Eren Ada, Claudia Solís-Lemus

Rendered from tanggle_vignette_espanol.Rmd in tanggle 1.13.0.
lineagespot User GuideUpdated 3 years ago

Nikolaos Pechlivanis, Maria Tsagiopoulou, Maria Christina Maniou, Anastasis Togkousidis, Evangelia Mouchtaropoulou, Taxiarchis Chassalevris, Serafeim Chaintoutis, Chrysostomos Dovas, Maria Petala, Margaritis Kostoglou, Thodoris Karapantsios, Stamatia Laidou, Elisavet Vlachonikola, Anastasia Chatzidimitriou, Agis Papadopoulos, Nikolaos Papaioannou, Anagnostis Argiriou, Fotis E. Psomopoulos

Rendered from lineagespot.Rmd in lineagespot 1.11.0.
CelliD VignetteUpdated 3 years ago

Akira Cortal, Antonio Rausell

Rendered from BioconductorVignette.Rmd in CelliD 1.15.0.
VaSP: Quantification and Visualization of Variations of Splicing in PopulationUpdated 3 years ago

Huihui Yu, Qian Du and Chi Zhang

Rendered from VaSP.Rmd in VaSP 1.19.0.
hmdbQuery: working with Human Metabolome Database (hmdb.ca)Updated 3 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from hmdbQuery.Rmd in hmdbQuery 1.27.0.
MBQN vignetteUpdated 3 years ago

Eva Brombacher

Rendered from MBQNpackage.Rmd in MBQN 2.19.0.
Genetic distance calculation from genotype shifts of markersUpdated 3 years ago

Ruqian Lyu

Rendered from getStarted.Rmd in comapr 1.11.0.
RiboDiPA R packageUpdated 3 years ago

Keren Li, Matthew Hope, Xiaozhong A. Wang, Ji-Ping Wang

Rendered from RiboDiPA.Rmd in RiboDiPA 1.15.0.
Crispr/Cas9 gRNA designUpdated 3 years ago

Aditya M Bhagwat

Rendered from crispr_grna_design.Rmd in multicrispr 1.17.0.
peakPantheR Graphical User InterfaceUpdated 3 years ago

Arnaud Wolfer

Rendered from peakPantheR-GUI.Rmd in peakPantheR 1.21.0.
Detection and visualization of cell-cell interactions using LRBase and scTensorUpdated 3 years ago

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

Rendered from scTensor.Rmd in scTensor 2.17.0.
seqcombo for visualizing genetic reassortmentUpdated 3 years ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from seqcombo.Rmd in seqcombo 1.29.0.
Generating Samples of Gene Expression Data with Variational AutoencodersUpdated 3 years ago

Dongmin Jung

Rendered from VAExprs.Rmd in VAExprs 1.13.0.
PCOSP: Pancreatic Cancer Overall Survival PredictorUpdated 3 years ago

Vandana Sandhu, Heewon Seo, Christopher Eeles, Benjamin Haibe-Kains

Rendered from PCOSP_model_analysis.Rmd in PDATK 1.15.0.
Install MEMEUpdated 3 years ago

Spencer Nystrom

Rendered from install_guide.Rmd in memes 1.15.0.
An R package for Reactome Pathway AnalysisUpdated 3 years ago

Guangchuang Yu

Rendered from ReactomePA.Rmd in ReactomePA 1.51.0.
Manual for the combi pacakageUpdated 3 years ago

Stijn Hawinkel

Rendered from combi.Rmd in combi 1.19.0.
cbpManager: Managing cancer studies and generating files for cBioPortalUpdated 3 years ago

Arsenij Ustjanzew

Rendered from intro.rmd in cbpManager 1.15.0.
HMMcopyUpdated 3 years ago

Daniel Lai

Rendered from HMMcopy.Rnw in HMMcopy 1.49.0.
UsingMLPUpdated 3 years ago

Tobias Verbeke

Rendered from UsingMLP.Rnw in MLP 1.55.0.
The tradeSeq workflowUpdated 3 years ago

Koen Van den Berge and Hector Roux de Bézieux

Rendered from tradeSeq.Rmd in tradeSeq 1.21.0.
Overview of ProteodiscoUpdated 3 years ago

Job van Riet, Wesley van de Geer and Harmen van de Werken

Rendered from Overview_ProteoDisco.Rmd in ProteoDisco 1.13.0.
Using CONDOR for community detection in bipartite graphsUpdated 3 years ago

John Platig

Rendered from CONDOR.Rmd in netZooR 1.11.0.
Alignment & batch integration of single cell data with corralmUpdated 3 years ago

Lauren Hsu, Aedin Culhane

Rendered from corralm_alignment.Rmd in corral 1.17.0.
Using DelayedMatrix with MultiAssayExperimentUpdated 3 years ago

MultiAssay Special Interest Group

Rendered from UsingHDF5Array.Rmd in MultiAssayExperiment 1.33.1.
Infer speciesUpdated 3 years ago

Author: Brian M. Schilder

Rendered from infer_species.Rmd in orthogene 1.13.0.
EnhancedVolcano: publication-ready volcano plots with enhanced colouring and labelingUpdated 3 years ago

Kevin Blighe, Sharmila Rana, Myles Lewis

Rendered from EnhancedVolcano.Rmd in EnhancedVolcano 1.25.0.
Manual for the RCM pacakageUpdated 3 years ago

Stijn Hawinkel

Rendered from RCMvignette.Rmd in RCM 1.23.0.
MultiBaC user's guideUpdated 3 years ago

Manuel Ugidos, Sonia Tarazona, Maria J. Nueda

Rendered from MultiBaC.Rmd in MultiBaC 1.17.0.
treekoRUpdated 3 years ago

Adam Chan, Ellis Patrick

Rendered from vignette.Rmd in treekoR 1.15.0.
Using synapsisUpdated 3 years ago

Lucy McNeill

Rendered from synapsis_tutorial.Rmd in synapsis 1.13.0.
Creating RCX from scratch Updated 3 years ago

Florian J. Auer

Rendered from Creating_RCX_from_scratch.Rmd in RCX 1.11.0.
Appendix: The RCX and CX Data ModelUpdated 3 years ago

Florian J. Auer

Rendered from Appendix_The_RCX_and_CX_Data_Model.Rmd in RCX 1.11.0.
CopyNumberPlots: create copy-number specific plots using karyoploteRUpdated 3 years ago

Bernat Gel ([email protected]); Miriam Magallon ([email protected])

Rendered from CopyNumberPlots.Rmd in CopyNumberPlots 1.23.0.
annotatr: Making sense of genomic regionsUpdated 3 years ago

Raymond G. Cavalcante

Rendered from annotatr-vignette.Rmd in annotatr 1.33.0.
MAGAR: Methylation-Aware Genotype Association in RUpdated 3 years ago

Michael Scherer

Rendered from MAGAR.Rmd in MAGAR 1.15.0.
Functions for Shiny app developmentUpdated 3 years ago

Zuguang Gu ( [email protected] )

Rendered from shiny_dev.Rmd in InteractiveComplexHeatmap 1.15.0.
Interactivate heatmaps indirectly generated by pheatmap(), heatmap.2() and heatmap()Updated 3 years ago

Zuguang Gu ( [email protected] )

Rendered from interactivate_indirect.Rmd in InteractiveComplexHeatmap 1.15.0.
A Shiny app for visualizing DESeq2 resultsUpdated 3 years ago

Zuguang Gu ( [email protected] )

Rendered from deseq2_app.Rmd in InteractiveComplexHeatmap 1.15.0.
InterCellar User GuideUpdated 3 years ago

Marta Interlandi

Rendered from user_guide.Rmd in InterCellar 2.13.0.
Share interactive heatmaps to collaboratorsUpdated 3 years ago

Zuguang Gu ( [email protected] )

Rendered from share.Rmd in InteractiveComplexHeatmap 1.15.0.
Power analysis for CyTOF experimentsUpdated 3 years ago

Anne-Maud Ferreira

Rendered from CyTOFpower.Rmd in CyTOFpower 1.13.0.
Select target genes for TAP-seqUpdated 3 years ago

Andreas Gschwind

Rendered from tapseq_target_genes.Rmd in TAPseq 1.19.0.
Microbial dIversity and Network Analysis with minaUpdated 3 years ago

Rui Guan

Rendered from mina.Rmd in mina 1.15.0.
AnnotationHub-style MeSH ORA Framework from BioC 3.14Updated 3 years ago

Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Itoshi Nikaido

Rendered from MeSH.Rmd in meshr 2.13.0.
Roadmap to prepare the input matrix for scTensorUpdated 3 years ago

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

Rendered from scTensor_1_Data_format_ID_Conversion.Rmd in scTensor 2.17.0.
How to reanalyze the results of scTensorUpdated 3 years ago

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

Rendered from scTensor_4_Reanalysis.Rmd in scTensor 2.17.0.
An Introduction to sangeranalyseRUpdated 3 years ago

Author: Kuan-Hao Chao ([email protected])

Rendered from sangeranalyseR.Rmd in sangeranalyseR 1.17.0.
TPP_introduction_2DUpdated 3 years ago

Dorothee Childs

Rendered from TPP_introduction_2D.Rnw in TPP 3.35.0.
Introduction to "universalmotif"Updated 3 years ago

Benjamin Jean-Marie Tremblay^[[email protected]]

Rendered from Introduction.Rmd in universalmotif 1.25.1.
Motif comparisons and P-valuesUpdated 3 years ago

Benjamin Jean-Marie Tremblay^[[email protected]]

Rendered from MotifComparisonAndPvalues.Rmd in universalmotif 1.25.1.
Introduction to QDNAseqUpdated 3 years ago

Daoud Sie

Rendered from QDNAseq.Rnw in QDNAseq 1.43.0.
DelayedDataFrame: an on-disk represention of DataFrameUpdated 3 years ago

Qian Liu, Hervé Pagès, Martin Morgan

Rendered from DelayedDataFrame.Rmd in DelayedDataFrame 1.23.0.
The discordant R Package: A Novel Approach to Differential CorrelationUpdated 3 years ago

Charlotte Siska, Max McGrath, Katerina Kechris

Rendered from Using_discordant.Rmd in discordant 1.31.0.
padma package: Quick-start guideUpdated 3 years ago

Andrea Rau

Rendered from padma.Rmd in padma 1.17.0.
Performing gene set enrichment analyses with sparrowUpdated 3 years ago

Steve Lianoglou

Rendered from sparrow.Rmd in sparrow 1.13.1.
cliProfiler VignettesUpdated 3 years ago

You Zhou, Kathi Zarnack

Rendered from cliProfilerIntroduction.Rmd in cliProfiler 1.13.0.
Identifying Biomarkers from an Exposure Variable with biotmleUpdated 3 years ago

Nima Hejazi

Rendered from exposureBiomarkers.Rmd in biotmle 1.31.0.
An introduction to biodbHmdbUpdated 3 years ago

Pierrick Roger

Rendered from biodbHmdb.Rmd in biodbHmdb 1.13.0.
Similarity Metrics EvaluationUpdated 3 years ago

Tim Daniel Rose

Rendered from similarity-metrics-evaluation.Rmd in mosbi 1.13.0.
Creating a new field for entries.Updated 3 years ago

Pierrick Roger

Rendered from new_entry_field.Rmd in biodb 1.15.0.
Manipulating entry objectsUpdated 3 years ago

Pierrick Roger

Rendered from entries.Rmd in biodb 1.15.0.
Creating a Scatterplot with TextureUpdated 3 years ago

Tejas Guha

Rendered from vignette.Rmd in scatterHatch 1.13.0.
Basic usage of the infinityFlow packageUpdated 3 years ago

Etienne Becht

Rendered from basic_usage.Rmd in infinityFlow 1.17.0.
miRLABUpdated 3 years ago

Thuc Duy Le

Rendered from miRLAB-vignette.Rmd in miRLAB 1.37.0.
VCFArray: DelayedArray objects with on-disk/remote VCF backendUpdated 3 years ago

Qian Liu, Martin Morgan

Rendered from VCFArray.Rmd in VCFArray 1.23.0.
Context specific functional scores for protein-protein interaction networksUpdated 3 years ago

Ana Galhoz, Denes Turei

Rendered from wppi_workflow.Rmd in wppi 1.15.0.
ggmsa-Getting StartedUpdated 3 years ago

Lang Zhou and GuangChuang Yu

Rendered from ggmsa.Rmd in ggmsa 1.13.0.
The cytoKernel user's guideUpdated 3 years ago

Tusharkanti Ghosh, Victor Lui, Pratyaydipta Rudra, Souvik Seal, Thao Vu, Elena Hsieh, Debashis Ghosh

Rendered from cytoKernel.Rmd in cytoKernel 1.13.0.
PCAtools: everything Principal Component AnalysisUpdated 3 years ago

Kevin Blighe, Aaron Lun

Rendered from PCAtools.Rmd in PCAtools 2.19.0.
gCrisprTools and the Analysis of Pooled Screening DataUpdated 3 years ago

Russell Bainer

Rendered from gCrisprTools_Vignette.Rmd in gCrisprTools 2.13.0.
Protein Interactions and Networks with Compounds based on Sequences using Deep LearningUpdated 3 years ago

Dongmin Jung

Rendered from DeepPINCS.Rmd in DeepPINCS 1.15.0.
Analysis of single-cell genomic data with celdaUpdated 3 years ago

Joshua Campbell, Zhe Wang, Shiyi Yang, Sean Corbett, Yusuke Koga

Rendered from celda.Rmd in celda 1.23.0.
preciseTAD VignetteUpdated 3 years ago

Spiro Stilianoudakis, Mikhail Dozmorov

Rendered from preciseTAD.Rmd in preciseTAD 1.17.0.
An introduction to scReClassify packageUpdated 3 years ago

Taiyun Kim

Rendered from scReClassify.Rmd in scReClassify 1.13.0.
single-sperm-co-analysisUpdated 3 years ago

Ruqian Lyu

Rendered from single-sperm-co-analysis.Rmd in comapr 1.11.0.
Consensus and differential peak calling with epigraHMMUpdated 3 years ago

Pedro L. Baldoni, Naim U. Rashid, Joseph G. Ibrahim

Rendered from epigraHMM.Rmd in epigraHMM 1.15.0.
An Introduction to Rbowtie2Updated 3 years ago

Zheng Wei and Wei Zhang

Rendered from Rbowtie2-Introduction.Rmd in Rbowtie2 2.13.0.
Visualization of imaging cytometry data in RUpdated 3 years ago

Nils Eling, Nicolas Damond, Tobias Hoch

Rendered from cytomapper.Rmd in cytomapper 1.19.0.
sigFeature: Significant feature selection using SVM-RFE & t-statisticUpdated 3 years ago

Pijush Das, Dr. Susanta Roychudhury, Dr. Sucheta Tripathy

Rendered from vignettes.Rmd in sigFeature 1.25.0.
Introduction to AnnotationHubDataUpdated 3 years ago

Lori Shepherd

Rendered from IntroductionToAnnotationHubData.Rmd in AnnotationHubData 1.37.0.
Recovering intra-sample doubletsUpdated 3 years ago

Aaron Lun

Rendered from recoverDoublets.Rmd in scDblFinder 1.21.0.
ASSET VignetteUpdated 3 years ago

Samsiddhi Bhattacharjee

Rendered from vignette.Rnw in ASSET 2.25.0.
The FEAST User's GuideUpdated 3 years ago

Kenong Su, Hao Wu

Rendered from FEAST.Rmd in FEAST 1.15.0.
Overview of the condiments workflowUpdated 3 years ago

Hector Roux de Bézieux

Rendered from condiments.Rmd in condiments 1.15.0.
More controls for the tests used in the condiments workflowUpdated 3 years ago

Hector Roux de Bézieux

Rendered from controls.Rmd in condiments 1.15.0.
tanggle: Visualization of phylogenetic networks in a ggplot2 frameworkUpdated 3 years ago

Klaus Schliep, Marta Vidal-García, Leann Biancani, Francisco Henao Diaz, Eren Ada, Claudia Solís-Lemus

Rendered from tanggle_vignette.Rmd in tanggle 1.13.0.
fCCAC VignetteUpdated 3 years ago

Pedro Madrigal

Rendered from fCCAC.Rnw in fCCAC 1.33.0.
Using DIGGITUpdated 3 years ago

Mariano J Alvarez

Rendered from diggit.Rnw in diggit 1.39.0.
svaRetro Quick OverviewUpdated 3 years ago

Ruining Dong

Rendered from svaRetro.Rmd in svaRetro 1.13.0.
DMCHMM: Differentially Methylated CpG using Hidden Markov ModelUpdated 3 years ago

Farhad Shokoohi

Rendered from DMCHMM.Rmd in DMCHMM 1.29.0.
levi - Landscape Expression Visualization InterfaceUpdated 3 years ago

Isabelle M. da Silva, José R. Pilan, Agnes A. S. Takeda, Jose L. Rybarczyk-Filho

Rendered from levi.Rmd in levi 1.25.0.
ADAM: Activity and Diversity Analysis ModuleUpdated 3 years ago

André L. Molan, Giordano B. S. Seco, Agnes A. S. Takeda, Jose L. Rybarczyk-Filho

Rendered from ADAM.Rmd in ADAM 1.23.0.
ADAMgui: Activity and Diversity Analysis Module Graphical User InterfaceUpdated 3 years ago

Giordano B. S. Seco, André L. Molan, Agnes A. S. Takeda, Jose L. Rybarczyk-Filho

Rendered from ADAMgui.Rmd in ADAMgui 1.23.0.
Hi-C data analysis using HiTCUpdated 3 years ago

Nicolas Servant

Rendered from HiC_analysis.Rnw in HiTC 1.51.0.
karyoploteR: plot customizable linear genomes displaying arbitrary dataUpdated 3 years ago

Bernat Gel ([email protected])

Rendered from karyoploteR.Rmd in karyoploteR 1.33.0.
TreeAndLeaf: A graph layout strategy for binary trees with focus on the leavesUpdated 3 years ago

Milena A Cardoso, Luis E A Rizzardi, Leonardo W Kume, Sheyla Trefflich, Clarice Groeneveld, Mauro A A Castro

Rendered from TreeAndLeaf.Rmd in TreeAndLeaf 1.19.0.
Outlier Protein and Phosphosite Target IdentifierUpdated 3 years ago

Abdulkadir Elmas

Rendered from analysis.Rmd in oppti 1.21.0.
Drug-Target InteractionsUpdated 3 years ago

Authors: Kevin Horan, Yuzhu Duan, Austin Leong, Dan Evans, Jamison McCorrison, Nicholas Schork and Thomas Girke

Rendered from drugTargetInteractions.Rmd in drugTargetInteractions 1.15.0.
transformGamPoi QuickstartUpdated 3 years ago

Constantin Ahlmann-Eltze

Rendered from transformGamPoi.Rmd in transformGamPoi 1.13.0.
Introduction to spatialDEUpdated 3 years ago

Davide Corso, Milan Malfait, Lambda Moses

Rendered from spatialDE.Rmd in spatialDE 1.13.0.
Introduction to the PGCA PackageUpdated 3 years ago

David Kepplinger, Mandeep Sasaki, Gabriela Cohen Freue

Rendered from intro.Rmd in pgca 1.31.0.
11 - ELMER: Use caseUpdated 3 years ago

Tiago Chedraoui Silva

Rendered from usecase.Rmd in ELMER 2.31.0.
rGenomeTracksUpdated 3 years ago

Omar Elashkar

Rendered from rGenomeTracks.Rmd in rGenomeTracks 1.13.0.
Interactively explore and visualize Single Cell RNA seq dataUpdated 3 years ago

Jayaram Kancherla, Kazi Tasnim Zinat, Héctor Corrada Bravo

Rendered from ExploreTreeViz.Rmd in scTreeViz 1.13.0.
IntramiRExploreR_Vignettes_ver05Updated 3 years ago

Surajit Bhattacharyal and Daniel N. Cox

Rendered from IntramiRExploreR_vignettes.Rmd in IntramiRExploreR 1.29.0.
Omixer: multivariate and reproducible randomization to proactively counter batch effects in omics studiesUpdated 3 years ago

Lucy Sinke, Davy Cats, Bas Heijmans

Rendered from omixer-vignette.Rmd in Omixer 1.17.0.
MeSH Enrichment and Semantic AnalysesUpdated 3 years ago

Guangchuang Yu

Rendered from meshes.Rmd in meshes 1.33.0.
An R interface to the ProteomeXchange repositoryUpdated 3 years ago

Laurent Gatto

Rendered from rpx.Rmd in rpx 2.15.0.
Beginner's guide to the "MLSeq" packageUpdated 3 years ago

Gokmen Zararsiz

Rendered from MLSeq.Rnw in MLSeq 2.25.0.
The ramr User's GuideUpdated 3 years ago

Oleksii Nikolaienko

Rendered from ramr.Rmd in ramr 1.15.0.
CRISPRseek VignetteUpdated 3 years ago

Lihua Julie Zhu

Rendered from CRISPRseek.Rnw in CRISPRseek 1.47.0.
MEAT (Muscle Epigenetic Age Test)Updated 3 years ago

Sarah Voisin

Rendered from MEAT.Rmd in MEAT 1.19.0.
Introduction to BASiCSUpdated 3 years ago

Catalina Vallejos, Nils Eling

Rendered from BASiCS.Rmd in BASiCS 2.19.0.
Analyzing Regulatory Impact Factors and Partial Correlation and Information TheoryUpdated 3 years ago

Carlos Alberto Oliveira de Biagi Junior, Ricardo Perecin Nociti, Breno Osvaldo Funicheli, João Paulo Bianchi Ximenez, Patrícia de Cássia Ruy, Marcelo Gomes de Paula, Rafael dos Santos Bezerra and Wilson Araújo da Silva Junior

Rendered from CeTF.Rmd in CeTF 1.19.0.
Analyzing Sequence Data using the GENESIS PackageUpdated 3 years ago

Stephanie M. Gogarten

Rendered from assoc_test_seq.Rmd in GENESIS 2.37.0.
Genetic Association Testing using the GENESIS PackageUpdated 3 years ago

Matthew P. Conomos

Rendered from assoc_test.Rmd in GENESIS 2.37.0.
Population Structure and Relatedness Inference using the GENESIS PackageUpdated 3 years ago

Matthew P. Conomos

Rendered from pcair.Rmd in GENESIS 2.37.0.
systemPipeShinyUpdated 3 years ago

Author: Le Zhang, Daniela Cassol, Ponmathi Ramasamy, Jianhai Zhang, Gordon Mosher and Thomas Girke

Rendered from systemPipeShiny.Rmd in systemPipeShiny 1.17.0.
Data Mining for RNA-seq data: normalization, features selection and classification - DaMiRseq packageUpdated 3 years ago

Mattia Chiesa

Rendered from DaMiRseq.Rnw in DaMiRseq 2.19.0.
Vignette illustrating the usage of gscreend on simulated dataUpdated 3 years ago

Katharina Imkeller

Rendered from gscreend_simulated_data.Rmd in gscreend 1.21.0.
scDataviz: single cell dataviz and downstream analysesUpdated 3 years ago

Kevin Blighe

Rendered from scDataviz.Rmd in scDataviz 1.17.0.
StructuralVariantAnnotation Quick OverviewUpdated 3 years ago

Ruining Dong, Daniel Cameron

Rendered from vignettes.Rmd in StructuralVariantAnnotation 1.23.0.
3.1 - Data input - Creating MAE objectUpdated 3 years ago

Tiago Chedraoui Silva

Rendered from analysis_data_input.Rmd in ELMER 2.31.0.
Introduction to scAnnotatRUpdated 3 years ago

Vy Nguyen

Rendered from classifying-cells.Rmd in scAnnotatR 1.13.0.
moanin: An R Package for Time Course RNASeq Data AnalysisUpdated 3 years ago

Nelle Varoquaux

Rendered from documentation.Rmd in moanin 1.15.0.
Using hiAnnotatorUpdated 3 years ago

Nirav V Malani

Rendered from Intro.Rmd in hiAnnotator 1.41.0.
fcScan: features cluster ScanUpdated 3 years ago

Abdullah El-Kurdi, Ghiwa Khalil, Georges Khazen, Pierre Khoueiry

Rendered from fcScan_vignette.Rmd in fcScan 1.21.0.
MeSH.dbUpdated 3 years ago

Koki Tsuyuzaki

Rendered from MeSHDbi.Rnw in MeSHDbi 1.43.0.
LRBaseDbiUpdated 3 years ago

Koki Tsuyuzaki

Rendered from LRBaseDbi.Rnw in LRBaseDbi 2.17.0.
Software for reckoning AnVIL/Terra usageUpdated 3 years ago

BJ Stubbs, Vincent J. Carey, rebjh/stvjc at channing.harvard.edu

Rendered from billing.Rmd in AnVILBilling 1.17.0.
cfDNAProUpdated 3 years ago

Haichao Wang

Rendered from cfDNAPro.Rmd in cfDNAPro 1.13.0.
Variant CallingUpdated 3 years ago

Benjamin Story

Rendered from overview.Rmd in mitoClone2 1.13.0.
RnBeads AnnotationUpdated 3 years ago

Fabian Mueller

Rendered from RnBeads_Annotations.Rnw in RnBeads 2.25.0.
SplicingFactoryUpdated 3 years ago

Péter Szikora, Tamás Pór, Endre Sebestyén

Rendered from SplicingFactory.Rmd in SplicingFactory 1.15.0.
Computation of phylogenetic trees and clustering of mutationsUpdated 3 years ago

Lars Velten

Rendered from clustering.Rmd in mitoClone2 1.13.0.
Use of colaUpdated 3 years ago

Zuguang Gu ([email protected])

Rendered from cola.Rmd in cola 2.13.0.
Introduction to STRUCT - STatistics in R using Class-based TemplatesUpdated 3 years ago

Gavin R Lloyd, Ralf J Weber

Rendered from struct_templates_and_helper_functions.Rmd in struct 1.19.0.
SCOPE: Single-cell Copy Number EstimationUpdated 3 years ago

Rujin Wang, Danyu Lin, Yuchao Jiang

Rendered from SCOPE_vignette.Rmd in SCOPE 1.19.0.
artMS: Analytical R Tools for Mass SpectrometryUpdated 3 years ago

David Jimenez-Morales

Rendered from artMS_vignette.Rmd in artMS 1.25.0.
Tensor arithmetic by DelayedTensor Updated 3 years ago

Koki Tsuyuzaki, Itoshi Nikaido

Rendered from DelayedTensor_2.Rmd in DelayedTensor 1.13.0.
Tensor decomposition by DelayedTensor Updated 3 years ago

Koki Tsuyuzaki, Itoshi Nikaido

Rendered from DelayedTensor_3.Rmd in DelayedTensor 1.13.0.
VeloViz VignetteUpdated 3 years ago

Lyla Atta

Rendered from vignette.Rmd in veloviz 1.13.0.
Vignette of the a4Classif packageUpdated 3 years ago

Laure Cougnaud

Rendered from a4Classif-vignette.Rmd in a4Classif 1.55.0.
The vignette for running scShapesUpdated 3 years ago

Malindrie Dharmaratne

Rendered from vignette_scShapes.Rmd in scShapes 1.13.0.
PsiNorm: a scalable normalization for single-cellRNA-seq dataUpdated 3 years ago

Matteo Borella, Chiara Romualdi, and Davide Risso

Rendered from PsiNorm.Rmd in scone 1.31.0.
Quick guideUpdated 3 years ago

Nicolò Rossi

Rendered from CIMICE_SHORT.Rmd in CIMICE 1.15.0.
HubPub: Help with publication of Hub packagesUpdated 3 years ago

Kayla Interdonato, Martin Morgan

Rendered from HubPub.Rmd in HubPub 1.15.0.
Using Monocle as input to tradeSeqUpdated 3 years ago

Koen Van den Berge and Hector Roux de Bézieux

Rendered from Monocle.Rmd in tradeSeq 1.21.0.
hypeRUpdated 3 years ago

Anthony Federico, Stefano Monti

Rendered from hypeR.Rmd in hypeR 2.5.0.
Getting started with the plyranges packageUpdated 3 years ago

Stuart Lee

Rendered from an-introduction.Rmd in plyranges 1.27.0.
The iPath User's GuideUpdated 3 years ago

Kenong Su, Steve Qin

Rendered from iPath.Rmd in iPath 1.13.0.
The qsmooth user's guideUpdated 3 years ago

Stephanie C. Hicks, Kwame Okrah, Joseph Paulson, John Quackenbush, Rafael A. Irizarry, Hector Corrada-Bravo

Rendered from qsmooth.Rmd in qsmooth 1.23.0.
GWENA - TutorialUpdated 3 years ago

Gwenaëlle Lemoine

Rendered from GWENA_guide.Rmd in GWENA 1.17.0.
Concept of DelayedTensor Updated 3 years ago

Koki Tsuyuzaki, Itoshi Nikaido

Rendered from DelayedTensor_1.Rmd in DelayedTensor 1.13.0.
Einsum operation by DelayedTensor Updated 3 years ago

Koki Tsuyuzaki, Itoshi Nikaido

Rendered from DelayedTensor_4.Rmd in DelayedTensor 1.13.0.
scanMiRApp: shiny app and related convenience functionsUpdated 3 years ago

Pierre-Luc Germain, Michael Soutschek, Fridolin Groß

Rendered from scanMiRApp.Rmd in scanMiRApp 1.13.0.
rTRM: an R package for the identification of transcription regulatory modules (TRMs)Updated 3 years ago

Diego Diez

Rendered from Introduction.Rmd in rTRM 1.45.0.
cBioPortalData: Data Build ErrorsUpdated 3 years ago

Marcel Ramos & Levi Waldron

Rendered from cBioPortalDataErrors.Rmd in cBioPortalData 2.19.1.
The quantro user's guideUpdated 3 years ago

Stephanie C. Hicks, Rafael Irizarry

Rendered from quantro.Rmd in quantro 1.41.0.
The ORFhunteR package: User’s manualUpdated 3 years ago

Vasily V. Grinev, Mikalai M. Yatskou, Victor V. Skakun, Maryna K. Chepeleva, Petr V. Nazarov

Rendered from ORFhunteR.Rmd in ORFhunteR 1.15.0.
The IndexedFst classUpdated 3 years ago

Pierre-Luc Germain

Rendered from IndexedFST.Rmd in scanMiRApp 1.13.0.
categoryCompare: High-throughput data meta-analysis using gene annotationsUpdated 3 years ago

Robert M. Flight

Rendered from categoryCompare_vignette.Rmd in categoryCompare 1.51.0.
HGC package manualUpdated 3 years ago

Zou Ziheng, Hua Kui

Rendered from HGC.Rmd in HGC 1.15.0.
Chromatin Segmentation Analysis Using segmenterUpdated 3 years ago

Mahmoud Ahmed

Rendered from segmenter.Rmd in segmenter 1.13.0.
An R package for sequenceUpdated 3 years ago

Arjun Kinstlick

Rendered from seq2pathwaypackage.Rnw in seq2pathway 1.39.0.
MethylSeekRUpdated 3 years ago

Lukas Burger

Rendered from MethylSeekR.Rnw in MethylSeekR 1.47.0.
Reproducible GSEA BenchmarkingUpdated 3 years ago

Ludwig Geistlinger

Rendered from GSEABenchmarkeR.Rmd in GSEABenchmarkeR 1.27.0.
SubCellBarCode: Integrated workflow for robust classification and visualization of spatial proteomeUpdated 3 years ago

Taner Arslan, Lukas Orre, Mattias Vesterlund, Yanbo Pan, Janne Lehtiö

Rendered from SubCellBarCode.Rmd in SubCellBarCode 1.23.0.
chipenrich: Gene Set Enrichment For ChIP-seq Peak DataUpdated 3 years ago

Ryan P. Welch, Chee Lee, Raymond G. Cavalcante, Chris Lee, Kai Wang, Laura J. Scott, Maureen A. Sartor

Rendered from chipenrich-vignette.Rmd in chipenrich 2.31.0.
Predicting m6A sites from miCLIP2 data with m6AboostUpdated 3 years ago

You Zhou, Kathi Zarnack

Rendered from m6AboosVignettes.Rmd in m6Aboost 1.13.0.
XNAString packageUpdated 3 years ago

Anna Górska, Marianna Plucinska, Łukasz Kiełpiński, Lykke Pedersen, Disa Theler, Peter H. Hagedorn

Rendered from XNAString_vignette.Rmd in XNAString 1.15.0.
BUScorrect_user_guideUpdated 3 years ago

Fangda Song

Rendered from BUSseq_user_guide.Rnw in BUSseq 1.13.0.
Loading user-provided dataUpdated 3 years ago

Nuno Saraiva-Agostinho

Rendered from custom_data.Rmd in psichomics 1.33.0.
Identifying Active and Alternative Promoters from RNA-Seq data with proActivUpdated 4 years ago

Joseph Lee, Deniz Demircioğlu, Jonathan Göke

Rendered from proActiv.Rmd in proActiv 1.17.0.
GOfuncR: Gene Ontology Enrichment Using FUNCUpdated 4 years ago

Steffi Grote

Rendered from GOfuncR.Rmd in GOfuncR 1.27.0.
Differential RNA structurome analysis using dStructUpdated 4 years ago

Krishna Choudhary, Sharon Aviran

Rendered from dStruct.Rmd in dStruct 1.13.0.
GSgalgoR user GuideUpdated 4 years ago

Martin E. Guerrero-Gimenez, Juan Manuel Fernandez-Muñoz, Carlos A. Catania

Rendered from GSgalgoR.rmd in GSgalgoR 1.17.0.
genefu: A Package for Breast Cancer Gene Expression AnalysisUpdated 4 years ago

Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus Schröder, Laia Pare, Joel S.Parker - &nc Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC27599, USA, Aleix Prat, Benjamin Haibe-Kains

Rendered from genefu.Rmd in genefu 2.39.0.
scPCA: Sparse contrastive principal component analysisUpdated 4 years ago

Philippe Boileau and Nima Hejazi

Rendered from scpca_intro.Rmd in scPCA 1.21.0.
Deconvolution of bulk RNA-seq data with granulatorUpdated 4 years ago

Vincent Kuettel, Sabina Pfister, Enrico Ferrero

Rendered from granulator.Rmd in granulator 1.15.0.
NetSAM User GuideUpdated 4 years ago

Zhiao Shi

Rendered from NetSAM.Rmd in NetSAM 1.47.0.
ChromSCapeUpdated 4 years ago

Pacome Prompsy, Pia Kirchmeier, Céline Vallot

Rendered from vignette.Rmd in ChromSCape 1.17.0.
A Walk-through of RiboRUpdated 4 years ago

Michael Geng, Hakan Ozadam, Can Cenik

Rendered from ribor.Rmd in ribor 1.19.0.
rWikiPathways and BridgeDbRUpdated 4 years ago

by Alexander Pico

Rendered from rWikiPathways-and-BridgeDbR.Rmd in rWikiPathways 1.27.0.
Case study: visual interface tutorialUpdated 4 years ago

Nuno Saraiva-Agostinho

Rendered from GUI_tutorial.Rmd in psichomics 1.33.0.
The biobtreeR users guideUpdated 4 years ago

Tamer Gür

Rendered from biobtreeR.Rmd in biobtreeR 1.19.0.
Spaniel 10X VisiumUpdated 4 years ago

Rachel Queen

Rendered from spaniel-vignette-tenX-import.Rmd in Spaniel 1.21.0.
Meta-analyses on p-values of various differential testsUpdated 4 years ago

Aaron Lun

Rendered from overview.Rmd in metapod 1.15.0.
BloodGen3Module: Modular Repertoire Analysis and VisualizationUpdated 4 years ago

Darawan Rinchai

Rendered from BloodGen3Module.Rmd in BloodGen3Module 1.15.0.
Effect size estimation with apeglmUpdated 4 years ago

Anqi Zhu, Joseph G. Ibrahim, and Michael I. Love

Rendered from apeglm.Rmd in apeglm 1.29.0.
CNVizUpdated 4 years ago

Rebecca Greenblatt ([email protected])

Rendered from CNViz.Rmd in CNViz 1.15.0.
systemPipeTools: Data VisualizationsUpdated 4 years ago

Author: Daniela Cassol and Thomas Girke

Rendered from systemPipeTools.Rmd in systemPipeTools 1.15.0.
RNA-Seq expression example Updated 4 years ago

Paul Harrison

Rendered from V4_airway.Rmd in weitrix 1.19.0.
methylGSA: Gene Set Analysis for DNA Methylation DatasetsUpdated 4 years ago

Xu Ren and Pei Fen Kuan

Rendered from methylGSA-vignette.Rmd in methylGSA 1.25.0.
MesKit: Analyze and Visualize Multi-region Whole-exome Sequencing DataUpdated 4 years ago

Mengni Liu

Rendered from MesKit.Rmd in MesKit 1.17.0.
Using quantiseqrUpdated 4 years ago

Federico Marini^[[email protected]], Francesca Finotello^[[email protected]]

Rendered from using_quantiseqr.Rmd in quantiseqr 1.15.0.
Training non default regression modelsUpdated 4 years ago

Etienne Becht

Rendered from training_non_default_regression_models.Rmd in infinityFlow 1.17.0.
User guide: immunotation packageUpdated 4 years ago

Katharina Imkeller

Rendered from immunotation_vignette.Rmd in immunotation 1.15.0.
Implement interactive heatmap from scratchUpdated 4 years ago

Zuguang Gu ( [email protected] )

Rendered from from_scratch.Rmd in InteractiveComplexHeatmap 1.15.0.
Introduction to awstUpdated 4 years ago

Davide Risso

Rendered from awst_intro.Rmd in awst 1.15.0.
diffUTRUpdated 4 years ago

Pierre-Luc Germain

Rendered from diffUTR.Rmd in diffUTR 1.15.0.
diffUTR - diffSplice2Updated 4 years ago

Stefan Gerber, Pierre-Luc Germain

Rendered from diffSplice2.Rmd in diffUTR 1.15.0.
ChIP-seq AnalysisUpdated 4 years ago

Spencer Nystrom

Rendered from integrative_analysis.Rmd in memes 1.15.0.
Denovo Motif Discovery Using DREMEUpdated 4 years ago

Spencer Nystrom

Rendered from core_dreme.Rmd in memes 1.15.0.
Motif Comparison using TomTomUpdated 4 years ago

Spencer Nystrom

Rendered from core_tomtom.Rmd in memes 1.15.0.
Motif Scanning using FIMOUpdated 4 years ago

Spencer Nystrom

Rendered from core_fimo.Rmd in memes 1.15.0.
Introduction to regionReportUpdated 4 years ago

Leonardo Collado-Torres

Rendered from regionReport.Rmd in regionReport 1.41.0.
derfinder quick start guideUpdated 4 years ago

Leonardo Collado-Torres

Rendered from derfinder-quickstart.Rmd in derfinder 1.41.0.
POWSC: power and sample size snalysis for single-cell RNA-seqUpdated 4 years ago

Kenong Su @Emory, Zhijin Wu @Brown, Hao Wu @Emory

Rendered from POWSC.Rmd in POWSC 1.15.0.
Analyzing UMI-4C data with UMI4CatsUpdated 4 years ago

Mireia Ramos-Rodríguez and Marc Subirana-Granés

Rendered from UMI4Cats.Rmd in UMI4Cats 1.17.0.
Generally Applicable Gene-set/Pathway AnalysisUpdated 4 years ago

Weijun Luo

Rendered from gage.Rnw in gage 2.57.0.
RNA-Seq Data Pathway and Gene-set Analysis WorkflowsUpdated 4 years ago

Weijun Luo

Rendered from RNA-seqWorkflow.Rnw in gage 2.57.0.
DelayedArrays of random valuesUpdated 4 years ago

Aaron Lun

Rendered from userguide.Rmd in DelayedRandomArray 1.15.0.
The cleanUpdTSeq user's guideUpdated 4 years ago

Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua J. Zhu

Rendered from cleanUpdTSeq.Rmd in cleanUpdTSeq 1.45.0.
The marr user's guideUpdated 4 years ago

Tusharkanti Ghosh, Max McGrath, Daisy Philtron, Katerina Kechris, Debashis Ghosh

Rendered from MarrVignette.Rmd in marr 1.17.0.
atSNP: affinity tests for regulatory SNP detectionUpdated 4 years ago

Chandler Zuo, Sunyoung Shin, Sunduz Keles

Rendered from atsnp-vignette.rmd in atSNP 1.23.0.
Running fedup with a single test setUpdated 4 years ago

Catherine Ross

Rendered from fedup_singleTest.rmd in fedup 1.15.0.
Running fedup with multiple test setsUpdated 4 years ago

Catherine Ross

Rendered from fedup_mutliTest.rmd in fedup 1.15.0.
Running fedup with two test setsUpdated 4 years ago

Catherine Ross

Rendered from fedup_doubleTest.rmd in fedup 1.15.0.
On disk storage and handling of imagesUpdated 4 years ago

Nils Eling

Rendered from cytomapper_ondisk.Rmd in cytomapper 1.19.0.
LOB/LOD Estimation WorkflowUpdated 4 years ago

Cyril Galitzine

Rendered from MSstatsLOBD_workflow.Rmd in MSstatsLOBD 1.15.0.
An introduction to PhosR packageUpdated 4 years ago

Taiyun Kim, Hani Jieun Kim, Di Xiao, Pengyi Yang

Rendered from PhosR.Rmd in PhosR 1.17.0.
Flexible clustering for BioconductorUpdated 4 years ago

Aaron Lun

Rendered from clusterRows.Rmd in bluster 1.17.0.
Transcriptomic Intelligent Pipeline: The KnowSeq user guide Updated 4 years ago

Daniel Castillo-Secilla, Juan Manuel Galvez, Marta Verona-Almeida, Francisco Carrillo-Perez, Francisco Manuel Ortuno, Luis Javier Herrera and Ignacio Rojas

Rendered from KnowSeq.Rmd in KnowSeq 1.21.0.
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communitiesUpdated 4 years ago

Pengfan Zhang

Rendered from Rbec.Rmd in Rbec 1.15.0.
Assorted clustering diagnosticsUpdated 4 years ago

Aaron Lun

Rendered from diagnostics.Rmd in bluster 1.17.0.
Detecting clusters of doublet cells with DE analysesUpdated 4 years ago

Aaron Lun

Rendered from findDoubletClusters.Rmd in scDblFinder 1.21.0.
Scoring potential doublets from simulated densitiesUpdated 4 years ago

Aaron Lun

Rendered from computeDoubletDensity.Rmd in scDblFinder 1.21.0.
Vignette for DominoEffect packageUpdated 4 years ago

Marija Buljan and Peter Blattmann

Rendered from Vignette.Rmd in DominoEffect 1.27.0.
ternarynet: A Computational Bayesian Approach to Ternary Network EstimationUpdated 4 years ago

McCall N. Matthew

Rendered from ternarynet.Rnw in ternarynet 1.51.0.
Using rcellminerUpdated 4 years ago

Augustin Luna

Rendered from rcellminerUsage.Rmd in rcellminer 2.29.0.
The hummingbirdUpdated 4 years ago

Eleni Adam, Tieming Ji, Desh Ranjan

Rendered from hummingbird.Rmd in hummingbird 1.17.0.
interacCircosUpdated 4 years ago

Zhe Cui

Rendered from interacCircos.Rmd in interacCircos 1.17.0.
Correcting batch effects in single-cell RNA-seq dataUpdated 4 years ago

Aaron Lun

Rendered from correction.Rmd in batchelor 1.23.0.
Using supersigsUpdated 4 years ago

Albert Kuo

Rendered from supersigs.Rmd in supersigs 1.15.0.
CytoGLMM WorkflowUpdated 4 years ago

Christof Seiler

Rendered from CytoGLMM.Rmd in CytoGLMM 1.15.0.
barcodetrackRUpdated 4 years ago

Diego A. Espinoza & Ryland D. Mortlock

Rendered from Introduction_to_barcodetrackR.Rmd in barcodetrackR 1.15.0.
Motif Enrichment Testing using AMEUpdated 4 years ago

Spencer Nystrom

Rendered from core_ame.Rmd in memes 1.15.0.
trackViewer Vignette: dandelionPlotUpdated 4 years ago

Jianhong Ou, Lihua Julie Zhu

Rendered from dandelionPlot.Rmd in trackViewer 1.43.1.
LRcell: Differential cell type change analysis using Logistic/linear Regression.Updated 4 years ago

Wenjing Ma, Dr. Zhaohui S. Qin

Rendered from LRcell-vignette.Rmd in LRcell 1.15.0.
ATACseqQC GuideUpdated 4 years ago

Jianhong Ou, Haibo Liu, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

Rendered from ATACseqQC.Rmd in ATACseqQC 1.31.0.
flowVS: Cell population matching and meta-clustering in Flow CytometryUpdated 4 years ago

Ariful Azad

Rendered from flowVS.Rnw in flowVS 1.39.0.
KBoostUpdated 4 years ago

Luis F. Iglesias-Martinez, Barbara De Kegel and Walter Kolch

Rendered from KBoost.Rmd in KBoost 1.15.0.
Tidying Motif MetadataUpdated 4 years ago

Spencer Nystrom

Rendered from tidy_motifs.Rmd in memes 1.15.0.
Fitting the models and additional control of fitGAM in tradeSeqUpdated 4 years ago

Koen Van den Berge and Hector Roux de Bézieux

Rendered from fitGAM.Rmd in tradeSeq 1.21.0.
MiDAS tutorialUpdated 4 years ago

Maciej Migdał & Christian Hammer

Rendered from MiDAS_tutorial.Rmd in midasHLA 1.15.0.
A brief introduction to decompTumor2SigUpdated 4 years ago

Rosario Michael Piro

Rendered from decompTumor2Sig.Rmd in decompTumor2Sig 2.23.0.
EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interfaceUpdated 4 years ago

Felix G.M. Ernst

Rendered from EpiTxDb.Rmd in EpiTxDb 1.19.0.
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulationUpdated 4 years ago

Kandarp Joshi

Rendered from epidecodeR.Rmd in epidecodeR 1.15.0.
Differential Topology: Comparing Conditions along a TrajectoryUpdated 4 years ago

Kelly Street and Koen Van den Berge

Rendered from conditionsVignette.Rmd in slingshot 2.15.0.
How interactive complex heatmap is implementedUpdated 4 years ago

Zuguang Gu ( [email protected] )

Rendered from implementation.Rmd in InteractiveComplexHeatmap 1.15.0.
Decorations on heatmapsUpdated 4 years ago

Zuguang Gu ( [email protected] )

Rendered from decoration.Rmd in InteractiveComplexHeatmap 1.15.0.
cellmigRationUpdated 4 years ago

Waldir Leoncio

Rendered from cellmigRation.Rmd in cellmigRation 1.15.0.
How to use Well Plate MakerUpdated 4 years ago

Helene Borges

Rendered from wpm_vignette.Rmd in wpm 1.17.0.
flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequencyUpdated 4 years ago

Alice Yue

Rendered from flowGraph.Rmd in flowGraph 1.15.0.
REDseq VignetteUpdated 4 years ago

Lihua Julie Zhu

Rendered from REDseq.Rnw in REDseq 1.53.0.
iCOBRA User GuideUpdated 4 years ago

Charlotte Soneson

Rendered from iCOBRA.Rmd in iCOBRA 1.35.0.
Gene Expression Variation Analysis (GEVA)Updated 4 years ago

Itamar José Guimarães Nunes^[Structural Bioinformatics and Computational Lab (SBCB) -- Federal University of Rio Grande do Sul (UFRGS)], Murilo Zanini David^[Graduate Program in Ecology -- Federal University of Rio Grande do Sul (UFRGS)], \linebreak, Bruno César Feltes\footnotemark[1], and Marcio Dorn\footnotemark[1]

Rendered from geva.Rmd in geva 1.15.0.
Bio Pipeline UsageUpdated 4 years ago

Dario Righelli

Rendered from bio_usage.rmd in easyreporting 1.19.0.
easyreporting standard usageUpdated 4 years ago

Dario Righelli

Rendered from standard_usage.rmd in easyreporting 1.19.0.
cyanoFilterUpdated 4 years ago

Olusoji O. D., Spaak J., Neyens T.,De Laender F., Aerts M.

Rendered from cyanoFilter.Rmd in cyanoFilter 1.15.0.
ExperimentSubset: Manages subsets of data with Bioconductor Experiment objectsUpdated 4 years ago

Irzam Sarfraz, Muhammad Asif, Joshua D. Campbell

Rendered from ExperimentSubset.Rmd in ExperimentSubset 1.17.0.
Using genomicInstabilityUpdated 4 years ago

Mariano Alvarez

Rendered from genomicInstability.Rnw in genomicInstability 1.13.0.
SBGNview Based Pathway Analysis and Visualization WorkflowUpdated 4 years ago

Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered from pathway.enrichment.analysis.Rmd in SBGNview 1.21.0.
Running SConESUpdated 4 years ago

Héctor Climente-González

Rendered from scones_usage.Rmd in martini 1.27.0.
Simulating SConES-based phenotypesUpdated 4 years ago

Héctor Climente-González

Rendered from simulate_phenotype.Rmd in martini 1.27.0.
Generating toy datasetsUpdated 4 years ago

Hector Roux de Bézieux

Rendered from examples.Rmd in condiments 1.15.0.
Converting BUS format into sparse matrixUpdated 4 years ago

Lambda Moses

Rendered from sparse-matrix.Rmd in BUSpaRse 1.21.0.
Old functions (deprecated)Updated 4 years ago

Alexander Ploner

Rendered from oldHeatplus.Rnw in Heatplus 3.15.0.
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomesUpdated 4 years ago

Ines de Santiago, Wei Liu, Ke Yuan, Florian Markowetz. University of Cambridge, Cancer Research UK Cambridge Institute

Rendered from BaalChIP.Rmd in BaalChIP 1.33.0.
SBGNview Quick StartUpdated 4 years ago

Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered from SBGNview.quick.start.Rmd in SBGNview 1.21.0.
SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway CollectionsUpdated 4 years ago

Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com

Rendered from SBGNview.Vignette.Rmd in SBGNview 1.21.0.
RcwlPipelines: Bioinformatics tools and pipelines based on RcwlUpdated 4 years ago

Qiang Hu, Qian Liu

Rendered from RcwlPipelines.Rmd in RcwlPipelines 1.23.0.
An Introduction to PDATK Classes and MethodsUpdated 4 years ago

Vandana Sandhu, Heewon Seo, Christopher Eeles, Benjamin Haibe-Kains

Rendered from PDATK_introduction.rmd in PDATK 1.15.0.
CONSTANdUpdated 4 years ago

Joris Van Houtven, Geert Jan Bex, Dirk Valkenborg

Rendered from CONSTANd.Rmd in CONSTANd 1.15.0.
PhenoGeneRankerUpdated 4 years ago

Cagatay Dursun, Jake Petrie

Rendered from PhenoGeneRanker.Rmd in PhenoGeneRanker 1.15.0.
ROSeqUpdated 4 years ago

Krishan Gupta

Rendered from ROSeq.Rmd in ROSeq 1.19.0.
| Epistatic Nested Effects Models: | Inferring mixed epistasis from indirect measurements of knock-out screensUpdated 4 years ago

Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz

Rendered from epiNEM.Rmd in epiNEM 1.31.0.
ComplexHeatmap vignetteUpdated 4 years ago

Zuguang Gu

Rendered from complex_heatmap.rmd in ComplexHeatmap 2.23.0.
MOGAMUNUpdated 4 years ago

Elva María Novoa del Toro

Rendered from MOGAMUN_Vignette.Rmd in MOGAMUN 1.17.0.
Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression DataUpdated 4 years ago

Timothy Tickle, Itay Tirosh, Christophe Georgescu, Maxwell Brown, Brian Haas

Rendered from inferCNV.Rmd in infercnv 1.23.0.
A likelihood maximization approach to infer the clonal structure of a cancer using multiple tumor samplesUpdated 4 years ago

Habil Zare

Rendered from Clonal_decomposition_by_Clomial.Rnw in Clomial 1.43.0.
Most probably asked questionsUpdated 4 years ago

Zuguang Gu

Rendered from most_probably_asked_questions.Rmd in ComplexHeatmap 2.23.0.
Random Rotation Package IntroductionUpdated 4 years ago

Peter Hettegger

Rendered from randRotationIntro.Rmd in randRotation 1.19.0.
Normalizing single-cell RNA-seq dataUpdated 4 years ago

Aaron Lun

Rendered from norm.Rmd in scuttle 1.17.0.
Quality control for single-cell RNA-seq dataUpdated 4 years ago

Aaron Lun

Rendered from qc.Rmd in scuttle 1.17.0.
Creating this HDF5 distributionUpdated 4 years ago

Mike L. Smith

Rendered from downloadHDF5.Rmd in Rhdf5lib 1.29.0.
Introduction To Bioconductor Annotation Packages Updated 4 years ago

Bioconductor Package Maintainer

Rendered from IntroToAnnotationPackages.Rnw in AnnotationDbi 1.69.0.
GlobalAncovaUpdated 4 years ago

Manuela Hummel

Rendered from GlobalAncova.rnw in GlobalAncova 4.25.0.
MiDAS quick startUpdated 4 years ago

Maciej Migdał & Christian Hammer

Rendered from MiDAS_vignette.Rmd in midasHLA 1.15.0.
Applying a function over a SingleCellExperiment's contentsUpdated 4 years ago

Aaron Lun

Rendered from apply.Rmd in SingleCellExperiment 1.29.1.
Example: finding E. coli outstanding genomic zones in response to nickel stressUpdated 4 years ago

Hua Zhong and Joe Song

Rendered from GenomicOZone.Rmd in GenomicOZone 1.21.0.
annaffy PrimerUpdated 4 years ago

Colin A. Smith

Rendered from annaffy.Rnw in annaffy 1.79.0.
Protein workflowUpdated 4 years ago

Petra Palenikova & Rick Scavetta

Rendered from proteinWorkflow.Rmd in ComPrAn 1.15.0.
SILAC complexomicsUpdated 4 years ago

Petra Palenikova & Rick Scavetta

Rendered from SILACcomplexomics.Rmd in ComPrAn 1.15.0.
fmcsR: Mismatch Tolerant Maximum Common Substructure Detection for Advanced Compound Similarity SearchingUpdated 4 years ago

Authors: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke

Rendered from fmcsR.Rmd in fmcsR 1.49.0.
eiR: Accelerated Similarity Searching of Small MoleculesUpdated 4 years ago

Authors: Kevin Horan, Yiqun Cao, Tyler Backman & Thomas Girke

Rendered from eiR.Rmd in eiR 1.47.0.
Using Categories to Analyze Microarray DataUpdated 4 years ago

Bioconductor Package Maintainer

Rendered from Category.Rnw in Category 2.73.0.
Combine TreeSummarizedExperiment objectsUpdated 4 years ago

Ruizhu HUANG, Charlotte Soneson, Mark Robinson

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Grouping Mass Spectrometry FeaturesUpdated 4 years ago

Johannes Rainer

Rendered from MsFeatures.Rmd in MsFeatures 1.15.0.
An introduction to the SingleCellExperiment classUpdated 4 years ago

Davide Risso, Aaron Lun

Rendered from intro.Rmd in SingleCellExperiment 1.29.1.
Developing around the SingleCellExperiment classUpdated 4 years ago

Davide Risso and Aaron Lun

Rendered from devel.Rmd in SingleCellExperiment 1.29.1.
Basic Functions for Flow Cytometry DataUpdated 4 years ago

Mike Jiang

Rendered from HowTo-flowCore.Rnw in flowCore 2.19.0.
Expression and Methylation Analysis with MEALUpdated 4 years ago

Carlos Ruiz, Juan R. González

Rendered from caseExample.Rmd in MEAL 1.37.0.
Methylation Analysis with MEALUpdated 4 years ago

Carlos Ruiz, Juan R. González

Rendered from MEAL.Rmd in MEAL 1.37.0.
SeqGate: Filter lowly expressed featuresUpdated 4 years ago

Christelle Reynès, Stéphanie Rialle

Rendered from Seqgate-html-vignette.Rmd in SeqGate 1.17.0.
Designing SD context with ModConUpdated 4 years ago

Johannes Ptok

Rendered from ModCon.Rmd in ModCon 1.15.0.
An introduction to mbkmeansUpdated 4 years ago

Yuwei Ni, Davide Risso, Stephanie Hicks, and Elizabeth Purdom

Rendered from Vignette.Rmd in mbkmeans 1.23.0.
Introduction to TreeSummarizedExperimentUpdated 4 years ago

Ruizhu HUANG, Charlotte Soneson, Mark Robinson

Rendered from Introduction_to_treeSummarizedExperiment.Rmd in TreeSummarizedExperiment 2.15.0.
ACE vignetteUpdated 4 years ago

Jos B. Poell

Rendered from ACE_vignette.Rmd in ACE 1.25.0.
03 - Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)Updated 4 years ago

Bioconductor Package Maintainer

Rendered from independent_filtering_plots.Rnw in genefilter 1.89.0.
The oposSOM users guideUpdated 4 years ago

Henry Loeffler-Wirth

Rendered from Vignette.Rnw in oposSOM 2.25.0.
SingleCellTrajectoryAnalysisUpdated 4 years ago

Anna Laddach and Michael Shapiro

Rendered from SingleCellTrajectoryAnalysis.Rmd in TrajectoryGeometry 1.15.0.
Matrix representations to support decompositionUpdated 4 years ago

Aaron Lun

Rendered from representations.Rmd in BiocSingular 1.23.0.
Commented package sourceUpdated 4 years ago

Alexander Ploner

Rendered from annHeatmapCommentedSource.Rnw in Heatplus 3.15.0.
Using BumpyMatrix objectsUpdated 4 years ago

Aaron Lun

Rendered from BumpyMatrix.Rmd in BumpyMatrix 1.15.0.
Computing q-values conditioned on covariates using swfdrUpdated 4 years ago

Simina M. Boca

Rendered from swfdrQ.Rmd in swfdr 1.33.0.
Input File DescriptionUpdated 4 years ago

Petra Palenikova & Rick Scavetta

Rendered from fileFormats.rmd in ComPrAn 1.15.0.
regutools: an R package for the extraction of gene regulatory networks from RegulonDBUpdated 4 years ago

Joselyn Chávez, Carmina Barberena Jonas, Jesus Emiliano Sotelo-Fonseca, Jose Alquicira Hernandez, Heladia Salgado, Leonardo Collado-Torres, Alejandro Reyes

Rendered from regutools.Rmd in regutools 1.19.0.
derfinder users guideUpdated 4 years ago

Leonardo Collado-Torres

Rendered from derfinder-users-guide.Rmd in derfinder 1.41.0.
GeneExpressionSignature: Computing pairwise distances between different biological statesUpdated 4 years ago

Yang Cao, Fei Li

Rendered from GeneExpressionSignature.Rmd in GeneExpressionSignature 1.53.0.
Utilities for basilisk installationUpdated 4 years ago

Aaron Lun

Rendered from purpose.Rmd in basilisk.utils 1.19.0.
arrayMvout -- multivariate outlier algorithm for expression arraysUpdated 4 years ago

V. Carey

Rendered from arrayMvout.Rnw in arrayMvout 1.65.0.
| Mixture Nested Effects Models: | Simultaneous inference of causal networks and corresponding subpopulations from single cell perturbation dataUpdated 4 years ago

Martin Pirkl, Niko Beerenwinkel

Rendered from mnem.Rmd in mnem 1.23.0.
| Boolean Nested Effects Models: | Inferring the logical signalling of pathways from indirect measurements and biological perturbations.Updated 4 years ago

Martin Pirkl

Rendered from bnem.rmd in bnem 1.15.0.
Censored covariate in cytometryUpdated 4 years ago

Reto Gerber

Rendered from censored_covariate.Rmd in censcyt 1.15.0.
crlmmDownstreamUpdated 4 years ago

Robert Scharpf

Rendered from crlmmDownstream.Rnw in VanillaICE 1.69.0.
Suppl. Ch. 5 - Visualizing the ResultsUpdated 4 years ago

Gabriel Odom

Rendered from Supplement5-Analyse_Results.Rmd in pathwayPCA 1.23.0.
snapcount vignetteUpdated 4 years ago

Christopher Wilks

Rendered from snapcount_vignette.Rmd in snapcount 1.19.0.
The LoomExperiment ClassesUpdated 4 years ago

Daniel Van Twisk

Rendered from LoomExperiment.Rmd in LoomExperiment 1.25.0.
coseq package: Quick-start guideUpdated 4 years ago

Andrea Rau, Antoine Godichon-Baggioni, and Cathy Maugis-Rabusseau

Rendered from coseq.Rmd in coseq 1.31.0.
Using appreci8RUpdated 4 years ago

Sarah Sandmann

Rendered from appreci8R.Rnw in appreci8R 1.25.0.
scGPS introductionUpdated 4 years ago

Quan Nguyen and Michael Thompson

Rendered from vignette.Rmd in scGPS 1.21.0.
Integrative Pathway Analysis with pathwayPCAUpdated 4 years ago

Gabriel Odom, Lily Wang, Xi Chen

Rendered from Introduction_to_pathwayPCA.Rmd in pathwayPCA 1.23.0.
Reporting on RNA-seq differential expressionUpdated 4 years ago

Jason A. Hackney

Rendered from rnaseqAnalysis.Rnw in ReportingTools 2.47.0.
Gene set enrichment analysis of RNA-Seq data with the SeqGSEA packageUpdated 4 years ago

Xi Wang

Rendered from SeqGSEA.Rnw in SeqGSEA 1.47.0.
Trajectory utilities for package developersUpdated 4 years ago

Aaron Lun

Rendered from overview.Rmd in TrajectoryUtils 1.15.0.
Introduction to RtpcaUpdated 4 years ago

Nils Kurzawa

Rendered from Rtpca.Rmd in Rtpca 1.17.0.
HTSFilter package: Quick-start guideUpdated 4 years ago

Andrea Rau, Mélina Gallopin, Gilles Celeux, Florence Jaffrézic

Rendered from HTSFilter.Rmd in HTSFilter 1.47.0.
Introducing the csaw packageUpdated 4 years ago

Aaron Lun

Rendered from csaw.Rmd in csaw 1.41.0.
Using the GEOfastq PackageUpdated 4 years ago

Alex Pickering

Rendered from GEOfastq.Rmd in GEOfastq 1.15.0.
DEsubsUpdated 4 years ago

Aristidis G. Vrahatis, Panos Balomenos

Rendered from DEsubs.Rmd in DEsubs 1.33.0.
About diffcoexpUpdated 4 years ago

Wenbin Wei

Rendered from diffcoexp.Rnw in diffcoexp 1.27.0.
Visualizing multiHiCcompare results in JuiceboxUpdated 4 years ago

John C. Stansfield & Mikhail G. Dozmorov

Rendered from juiceboxVisualization.Rmd in multiHiCcompare 1.25.0.
multiHiCcompare VignetteUpdated 4 years ago

John C. Stansfield & Mikhail G. Dozmorov

Rendered from multiHiCcompare.Rmd in multiHiCcompare 1.25.0.
Analysing SNVs with VarConUpdated 4 years ago

Johannes Ptok

Rendered from VarCon.Rmd in VarCon 1.15.0.
shinyÉPICo: the user's guideUpdated 4 years ago

Octavio Morante-Palacios, Esteban Ballestar

Rendered from shiny_epico.Rmd in shinyepico 1.15.0.
Process scRNA-Seq reads in scruffUpdated 4 years ago

Zhe Wang

Rendered from scruff.Rmd in scruff 1.25.0.
The transcriptogramer user's guideUpdated 4 years ago

Diego Morais, Rodrigo Dalmolin

Rendered from transcriptogramer.Rmd in transcriptogramer 1.29.0.
glmGamPoi QuickstartUpdated 4 years ago

Constantin Ahlmann-Eltze

Rendered from glmGamPoi.Rmd in glmGamPoi 1.19.0.
Quick analysis of nucleosome positioning experiments using the nucleR packageUpdated 4 years ago

Oscar Flores Guri

Rendered from nucleR.Rmd in nucleR 2.39.0.
interactiveDisplay: A package for enabling interactive visualization of Bioconductor objectsUpdated 4 years ago

Bioconductor Package Maintainer

Rendered from interactiveDisplay.Rnw in interactiveDisplay 1.45.0.
parody: parametric and resistant outlier dytectionUpdated 4 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from parody.Rmd in parody 1.65.0.
An introduction to SimFFPEUpdated 4 years ago

Lanying Wei

Rendered from SimFFPE.Rnw in SimFFPE 1.19.0.
An introduction to FilterFFPEUpdated 4 years ago

Lanying Wei

Rendered from FilterFFPE.Rnw in FilterFFPE 1.17.0.
SIAMCAT input files formatsUpdated 4 years ago

Konrad Zych, Jakob Wirbel, and Georg Zeller

Rendered from SIAMCAT_read-in.Rmd in SIAMCAT 2.11.0.
RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.Updated 4 years ago

Clarice S Groeneveld, Vinícius S Chagas, Gordon Robertson, Kerstin B Meyer, Mauro AA Castro.

Rendered from RTNsurvival.Rmd in RTNsurvival 1.31.0.
新手指引Updated 4 years ago

Jiefei Wang

Rendered from quick_start_guide_Chinese.Rmd in SharedObject 1.21.0.
RLassoCoxUpdated 4 years ago

Wei Liu

Rendered from RLassoCox.Rnw in RLassoCox 1.15.0.
parglms: fitting generalized linear and related models with parallel evaluation of contributions to sufficient statisticsUpdated 4 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from parglms.Rmd in parglms 1.39.0.
Methrix tutorialUpdated 4 years ago

CompEpigen

Rendered from methrix.Rmd in methrix 1.21.0.
vtpnet: variant-transcription factor-network toolsUpdated 4 years ago

VJ Carey

Rendered from vtpnet.Rnw in vtpnet 0.47.0.
Using AssessORFUpdated 4 years ago

Deepank Korandla

Rendered from UsingAssessORF.Rmd in AssessORF 1.25.0.
ADImpute tutorialUpdated 4 years ago

Ana Carolina Leote

Rendered from ADImpute_tutorial.Rmd in ADImpute 1.17.0.
GSgalgoR Callbacks MechanismUpdated 4 years ago

Carlos Catania

Rendered from GSgalgoR_callbacks.rmd in GSgalgoR 1.17.0.
msImpute: Imputation of peptide intensity by low-rank approximationUpdated 4 years ago

Soroor Hediyeh-zadeh, Andrew I. Webb, Melissa J. Davis

Rendered from msImpute-vignette.Rmd in msImpute 1.17.0.
wavClusteR: a workflow for PAR-CLIP data analysisUpdated 4 years ago

Federico Comoglio and Cem Sievers

Rendered from wavCluster_vignette.Rmd in wavClusteR 2.41.0.
Build functional gene modules with GNET2Updated 4 years ago

Chen Chen

Rendered from run_gnet2.Rmd in GNET2 1.23.0.
Working with multiple conditionsUpdated 4 years ago

Kelly Street, Koen Van den Berge and Hector Roux de Bézieux

Rendered from multipleConditions.Rmd in tradeSeq 1.21.0.
Vignette of the a4Preproc packageUpdated 4 years ago

Laure Cougnaud

Rendered from a4Preproc-vignette.Rmd in a4Preproc 1.55.0.
Vignette of the a4Reporting packageUpdated 4 years ago

Laure Cougnaud

Rendered from a4reporting-vignette.Rmd in a4Reporting 1.55.0.
Complete Guide for Seven Bridges API R ClientUpdated 4 years ago

Phil Webster

Rendered from api.Rmd in sevenbridges 1.37.0.
Vignette of the a4Core packageUpdated 4 years ago

Laure Cougnaud

Rendered from a4Core-vignette.Rmd in a4Core 1.55.0.
Introduction to Multivariate Analysis of Gene Expression Data using MADE4Updated 4 years ago

Aedin Culhane

Rendered from introduction.Rmd in made4 1.81.0.
Yeast gatingUpdated 4 years ago

R Clay Wright

Rendered from gating-vignette.Rmd in flowTime 1.31.0.
tomoda for tomo-seq data analysisUpdated 4 years ago

Wendao Liu

Rendered from tomoda.Rmd in tomoda 1.17.0.
Overview of Scry MethodsUpdated 4 years ago

Will Townes

Rendered from scry.Rmd in scry 1.19.0.
Scry Methods For Larger DatasetsUpdated 4 years ago

Will Townes

Rendered from bigdata.Rmd in scry 1.19.0.
Running the mdp packageUpdated 4 years ago

Helder Nakaya

Rendered from my-vignette.Rmd in mdp 1.27.0.
4.1 - Scatter plotsUpdated 4 years ago

Tiago Chedraoui Silva

Rendered from plots_scatter.Rmd in ELMER 2.31.0.
4.5 - Heatmap plotsUpdated 4 years ago

Tiago Chedraoui Silva

Rendered from plots_heatmap.Rmd in ELMER 2.31.0.
5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUIUpdated 4 years ago

Tiago Chedraoui Silva

Rendered from analysis_gui.Rmd in ELMER 2.31.0.
MOFA+: downstream analysis in RUpdated 4 years ago

Ricard Argelaguet, Britta Velten

Rendered from downstream_analysis.Rmd in MOFA2 1.17.0.
Introduction to Coordinate Covariation AnalysisUpdated 4 years ago

John Lawson

Rendered from IntroToCOCOA.Rmd in COCOA 2.21.0.
Detection of de novo copy number alterations in case-parent triosUpdated 4 years ago

Robert Scharpf

Rendered from MinimumDistance.Rnw in MinimumDistance 1.51.0.
RTCGAToolboxUpdated 4 years ago

Mehmet Kemal Samur

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Visualization of gene expression with NebulosaUpdated 4 years ago

Jose Alquicira-Hernandez

Rendered from introduction.Rmd in Nebulosa 1.17.0.
A quick introduction to GRanges and GRangesList objects (slides) Updated 4 years ago

Hervé Pagès

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A quick overview of the S4 class systemUpdated 4 years ago

Hervé Pagès

Rendered from S4QuickOverview.Rnw in S4Vectors 0.45.2.
Introduction to rnaEditrUpdated 4 years ago

Lanyu Zhang, Gabriel Odom, Lily Wang

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Using Microbiome Explorer application to analyze amplicon sequencing dataUpdated 4 years ago

Janina Reeder

Rendered from exploreMouseData.Rmd in microbiomeExplorer 1.17.0.
BioNet TutorialUpdated 4 years ago

Marcus Dittrich

Rendered from Tutorial.Rnw in BioNet 1.67.0.
SWATH2stats example scriptUpdated 4 years ago

Peter Blattmann

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3CPET: Finding Co-factor Complexes maintaining Chia-PET interactionsUpdated 4 years ago

Mohamed Nadhir Djekidel

Rendered from R3CPET.Rnw in R3CPET 1.39.0.
An Ultra-Fast All-in-One FASTQ preprocessorUpdated 4 years ago

Wei Wang [email protected]

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Working with MSstatsConvertUpdated 4 years ago

Mateusz Staniak

Rendered from msstats_data_format.Rmd in MSstatsConvert 1.17.0.
WorkflowUpdated 4 years ago

Ahmed Mohamed

Rendered from workflow.Rmd in lipidr 2.21.0.
Introduction to r BiocStyle::Biocpkg('DiscoRhythm')Updated 4 years ago

Matthew Carlucci, Algimantas Kriščiūnas, Haohan Li, Povilas Gibas, Karolis Koncevičius, Art Petronis, Gabriel Oh

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Comparing methods for differential expression analysis of RNAseq data with the compcodeR packageUpdated 4 years ago

Charlotte Soneson

Rendered from compcodeR.Rmd in compcodeR 1.43.0.
Dimensionality reduction and batch effect removal using NewWaveUpdated 4 years ago

Federico Agostinis

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Identifying DMCs using Bayesian functional regressions in BS-Seq dataUpdated 4 years ago

Farhad Shokoohi

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IONiseRUpdated 4 years ago

Mike L. Smith

Rendered from IONiseR.Rmd in IONiseR 2.31.0.
MPFEUpdated 4 years ago

Conrad Burden

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pageRankUpdated 4 years ago

Hongxu Ding

Rendered from introduction.rnw in pageRank 1.17.0.
How to interpret the HTML report generated by cellCellReport functionUpdated 4 years ago

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

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How to perform CCI simulation by cellCellSimulate functionUpdated 4 years ago

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

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ggtree: tree visualization and annotationUpdated 4 years ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from ggtree.Rmd in ggtree 3.15.0.
The rsemmed User's GuideUpdated 4 years ago

Leslie Myint

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TEQCUpdated 4 years ago

Sarah Bonnin

Rendered from TEQC.Rnw in TEQC 4.29.0.
DOSE: Disease Ontology Semantic and Enrichment analysisUpdated 4 years ago

Guangchuang Yu

Rendered from DOSE.Rmd in DOSE 4.1.0.
GO Semantic Similarity AnalysisUpdated 4 years ago

Guangchuang Yu

Rendered from GOSemSim.Rmd in GOSemSim 2.33.0.
The Chip Analysis Methylation PipelineUpdated 4 years ago

Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, and Andrew E Teschendorff

Rendered from ChAMP.Rmd in ChAMP 2.37.0.
rfaRmUpdated 4 years ago

Lara Selles Vidal

Rendered from ncRNAtools.Rmd in ncRNAtools 1.17.0.
VariantFiltering: filter coding and non-coding genetic variantsUpdated 4 years ago

Robert Castelo

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periodicDNAUpdated 4 years ago

Jacques Serizay

Rendered from periodicDNA.Rmd in periodicDNA 1.17.0.
Genome arithmeticsUpdated 4 years ago

Aditya M Bhagwat

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Prime EditingUpdated 4 years ago

Aditya M Bhagwat

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Correlation of epigenetic signals and genes in TADsUpdated 4 years ago

Konstantin Okonechnikov

Rendered from InTAD.Rmd in InTAD 1.27.0.
The pipeComp frameworkUpdated 4 years ago

Pierre-Luc Germain

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Multi-subject scRNA-seq AnalysisUpdated 4 years ago

Jason Ratcliff, Andrew Thurman, Michael Chimenti, Alejandro Pezzulo

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Concepts and practical details Updated 4 years ago

Paul Harrison

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dagLogo VignetteUpdated 4 years ago

Jianhong Ou, Haibo Liu, Lihua Julie Zhu

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Spectrum Motif Analysis (SPMA)Updated 4 years ago

Konstantin Krismer

Rendered from spma.Rmd in transite 1.25.0.
nearBynding VignetteUpdated 4 years ago

Veronica Busa

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Analyzing MPRA data with MPRAnalyzeUpdated 4 years ago

Tal Ashuach

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Visualization of gene expression with Nebulosa (in Seurat)Updated 4 years ago

Jose Alquicira-Hernandez

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Functional analysis of mouse mammary gland RNA-SeqUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

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BiocSet: Representing Element Sets in the TidyverseUpdated 4 years ago

Kayla Morrell, Martin Morgan

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An overview of ViSEAGO: Visualisation, Semantic similarity, Enrichment Analysis of Gene Ontology.Updated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

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Preparing an Alternative Splicing Annotation for psichomicsUpdated 4 years ago

Nuno Saraiva Agostinho

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Functional analysis of mouse mammary gland RNA-Seq using fgsea instead of topGOUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

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Evaluate impact of Semantic Similiarity choiceUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

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Handling Modifications with MSnIDUpdated 4 years ago

Vlad Petyuk

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Generating Grey Lists from Input LibrariesUpdated 4 years ago

Matt Eldridge

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Introduction to sparsenetglsUpdated 4 years ago

Irene SL Zeng and Thomas Lumley

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The scRNA PipelineDefinitionUpdated 4 years ago

Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson

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Using ssPATHSUpdated 4 years ago

Natalie R. Davidson

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MSnID Package for Handling MS/MS IdentificationsUpdated 4 years ago

Vlad Petyuk

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RegEnrich: an R package for gene regulator enrichment analysisUpdated 4 years ago

Weiyang Tao, Aridaman Pandit

Rendered from RegEnrich.Rmd in RegEnrich 1.17.0.
Assessing ChIP-seq sample quality with ChIPQCUpdated 4 years ago

Tom Carroll

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rBiopaxParser VignetteUpdated 4 years ago

Frank Kramer

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Utilities for handling droplet-based single-cell RNA-seq dataUpdated 4 years ago

Aaron Lun

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Introduction to decontamUpdated 4 years ago

Benjamin Callahan, Nicole Davis

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ldblock package: linkage disequilibrium data structuresUpdated 4 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

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Annotation for unannotated single-cell RNA-Seq data by scTGIFUpdated 4 years ago

Koki Tsuyuzaki, Itoshi Nikaido

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GenomeInfoDb: Introduction to GenomeInfoDbUpdated 4 years ago

Hervé Pagès

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RNAAgeCalc: A multi-tissue transcriptional age calculatorUpdated 4 years ago

Xu Ren and Pei Fen Kuan

Rendered from RNAAge-vignette.Rmd in RNAAgeCalc 1.19.0.
BLMAUpdated 4 years ago

Van-Dung Pham

Rendered from BLMA.Rnw in BLMA 1.31.0.
Deploying ExploreModelMatrix on a Shiny ServerUpdated 4 years ago

Charlotte Soneson, Federico Marini, Michael I Love, Florian Geier and Michael B Stadler

Rendered from EMMdeploy.Rmd in ExploreModelMatrix 1.19.0.
A DelayedArray backend for TileDBUpdated 4 years ago

Aaron Lun

Rendered from userguide.Rmd in TileDBArray 1.17.0.
IMMANUpdated 4 years ago

Minoo Ashtiani, Payman Nickchi, Abdollah Safari, Mehdi Mirzaie, Mohieddin Jafari

Rendered from IMMAN.Rmd in IMMAN 1.27.0.
GSEAminingUpdated 4 years ago

Oriol Arqués

Rendered from GSEAmining.Rmd in GSEAmining 1.17.0.
Cluster and impute scBS-seq data using MelissaUpdated 4 years ago

Andreas C. Kapourani, Guido Sanguinetti

Rendered from run_melissa.Rmd in Melissa 1.23.0.
Process and filter scBS-seq dataUpdated 4 years ago

Andreas C. Kapourani, Guido Sanguinetti

Rendered from process_files.Rmd in Melissa 1.23.0.
Modelling methylation profilesUpdated 4 years ago

Andreas C. Kapourani, Guido Sanguinetti

Rendered from BPRMeth_vignette.Rmd in BPRMeth 1.33.0.
Introduction to wiggleplotrUpdated 4 years ago

Kaur Alasoo

Rendered from wiggleplotr.Rmd in wiggleplotr 1.31.0.
Fetch homozygous genotypes of inbred mouse strainsUpdated 4 years ago

Matthias Munz

Rendered from fetch.Rmd in MouseFM 1.17.0.
Finemapping of genetic regions in inbred miceUpdated 4 years ago

Matthias Munz

Rendered from finemap.Rmd in MouseFM 1.17.0.
Prioritization of inbred mouse strains for resolving genetic regionsUpdated 4 years ago

Matthias Munz

Rendered from prio.Rmd in MouseFM 1.17.0.
An introduction to OTUbaseUpdated 4 years ago

Daniel Beck

Rendered from Introduction_to_OTUbase.Rnw in OTUbase 1.57.0.
Example of a cytometry data analysis with DepecheRUpdated 4 years ago

Jakob Theorell

Rendered from DepecheR_test.Rmd in DepecheR 1.23.0.
cn.mops: Manual for the R packageUpdated 4 years ago

Gundula Povysil

Rendered from cn.mops.Rnw in cn.mops 1.53.0.
The goSTAG User's GuideUpdated 4 years ago

Brian D. Bennett and Pierre R. Bushel

Rendered from goSTAG.Rmd in goSTAG 1.31.0.
Describe and Execute CWL Tools/Workflows in RUpdated 4 years ago

Phil Webster

Rendered from apps.Rmd in sevenbridges 1.37.0.
BEARscc: Using spike-ins to assess single cell cluster robustnessUpdated 4 years ago

David T. Severson

Rendered from BEARscc.Rmd in BEARscc 1.27.0.
Using interactiveDisplayBase for Bioconductor object visualization and modificationUpdated 4 years ago

Bioconductor Package Maintainer

Rendered from interactiveDisplayBase.Rmd in interactiveDisplayBase 1.45.0.
The multiMiR user's guideUpdated 4 years ago

Yuanbin Ru, Matt Mulvahill, Spencer Mahaffey, Katerina Kechris

Rendered from multiMiR.Rmd in multiMiR 1.29.0.
EDASeq: Exploratory Data Analysis and Normalization for RNA-SeqUpdated 5 years ago

Davide Risso

Rendered from EDASeq.Rmd in EDASeq 2.41.0.
getDEE2: Programmatic access to the DEE2 RNA expression datasetUpdated 5 years ago

Mark Ziemann & Antony Kaspi

Rendered from getDEE2.Rmd in getDEE2 1.17.0.
DEsingleUpdated 5 years ago

Zhun Miao

Rendered from DEsingle.Rmd in DEsingle 1.27.0.
Overview of the genomeIntervals package.Updated 5 years ago

Julien Gagneur

Rendered from genomeIntervals.Rnw in genomeIntervals 1.63.0.
Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq dataUpdated 5 years ago

Joris Meys

Rendered from SPsimSeq.Rmd in SPsimSeq 1.17.0.
Qtlizer: comprehensive QTL annotation of GWAS resultsUpdated 5 years ago

Julia Remes & Matthias Munz

Rendered from Qtlizer.Rmd in Qtlizer 1.21.0.
sparseMatrixStatsUpdated 5 years ago

Constantin Ahlmann-Eltze

Rendered from sparseMatrixStats.Rmd in sparseMatrixStats 1.19.0.
Sequence logos for DNA sequence alignmentsUpdated 5 years ago

Oliver Bembom, Robert Ivánek

Rendered from seqLogo.Rmd in seqLogo 1.73.0.
GWAS catalog: Phenotypes systematized by the experimental factor ontologyUpdated 5 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from gwascatOnt.Rmd in gwascat 2.39.0.
Input data formatsUpdated 5 years ago

Kellen Cresswell, Mikhail Dozmorov

Rendered from Input_Data.Rmd in TADCompare 1.17.0.
TAD comparison between two conditionsUpdated 5 years ago

Kellen Cresswell, Mikhail Dozmorov

Rendered from TADCompare.Rmd in TADCompare 1.17.0.
MOMA - Multi Omic Master Regulator AnalysisUpdated 5 years ago

Sunny Jones, Evan Paull, Mariano Alvarez, Federico Giorgi and Andrea Califano

Rendered from moma.Rmd in MOMA 1.19.0.
The DEA PipelineDefinitionUpdated 5 years ago

Pierre-Luc Germain

Rendered from pipeComp_dea.Rmd in pipeComp 1.17.0.
AlphaBetaUpdated 5 years ago

Y.Shahryary, Rashmi Hazarika, Frank Johannes

Rendered from AlphaBeta.Rmd in AlphaBeta 1.21.0.
Peak Matrix Processing for metabolomics datasetsUpdated 5 years ago

Andris Jankevics, Ralf Johannes Maria Weber

Rendered from pmp_vignette_peak_matrix_processing_for_metabolomics_datasets.Rmd in pmp 1.19.0.
ChIPCompUpdated 5 years ago

Li Chen

Rendered from ChIPComp.Rnw in ChIPComp 1.37.0.
ConsensusClusterPlus TutorialUpdated 5 years ago

Matt Wilkerson

Rendered from ConsensusClusterPlus.Rnw in ConsensusClusterPlus 1.71.0.
Signal drift and batch effect correction and mass spectral quality assessmentUpdated 5 years ago

Andris Jankevics, Gavin Rhys Lloyd, Ralf Johannes Maria Weber

Rendered from pmp_vignette_sbc_spectral_quality_assessment.Rmd in pmp 1.19.0.
Signal drift and batch effect correction for mass spectrometryUpdated 5 years ago

Andris Jankevics, Ralf Johannes Maria Weber

Rendered from pmp_vignette_signal_batch_correction_mass_spectrometry.Rmd in pmp 1.19.0.
optimalFlow: optimal-transport approach to Flow Cytometry analysisUpdated 5 years ago

Hristo Inouzhe

Rendered from optimalFlow_vignette.Rmd in optimalFlow 1.19.0.
OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic DataUpdated 5 years ago

Hamed Haseli Mashhadi ([email protected])

Rendered from OpenStats.Rmd in OpenStats 1.19.0.
Performing scClassify using pretrained modelUpdated 5 years ago

Yingxin Lin

Rendered from pretrainedModel.Rmd in scClassify 1.19.0.
scClassify Model Building and PredictionUpdated 5 years ago

Yingxin Lin

Rendered from scClassify.Rmd in scClassify 1.19.0.
countsimQC - Comparing characteristic features across count data setsUpdated 5 years ago

Charlotte Soneson

Rendered from countsimQC.Rmd in countsimQC 1.25.0.
Example report using bumphunter resultsUpdated 5 years ago

Leonardo Collado-Torres

Rendered from bumphunterExample.Rmd in regionReport 1.41.0.
receptLossUpdated 5 years ago

Daniel G. Piqué, John Greally, and Jessica Mar

Rendered from receptLoss.Rmd in receptLoss 1.19.0.
GLADUpdated 5 years ago

Philippe Hupe

Rendered from GLAD.Rnw in GLAD 2.71.0.
MotifDbUpdated 5 years ago

Paul Shannon

Rendered from MotifDb.Rmd in MotifDb 1.49.0.
An Introduction to intansvUpdated 5 years ago

Wen Yao

Rendered from intansvOverview.Rnw in intansv 1.47.0.
4.3 - Motif enrichment plotsUpdated 5 years ago

Tiago Chedraoui Silva

Rendered from plots_motif_enrichment.Rmd in ELMER 2.31.0.
3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact wayUpdated 5 years ago

Tiago Chedraoui Silva

Rendered from pipe.Rmd in ELMER 2.31.0.
GARS: a Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasetsUpdated 5 years ago

Mattia Chiesa

Rendered from GARS.Rnw in GARS 1.27.0.
Spatial quantile normalization for co-expression analysisUpdated 5 years ago

Yi Wang, Kasper D. Hansen

Rendered from spqn.Rmd in spqn 1.19.0.
Package Vignette for Genomic Interactions: ChIA-PET dataUpdated 5 years ago

Malcolm Perry

Rendered from chiapet_vignette.rmd in GenomicInteractions 1.41.0.
HiC vignette for GenomicInteractions packageUpdated 5 years ago

Liz Ing-Simmons

Rendered from hic_vignette.Rmd in GenomicInteractions 1.41.0.
GGPAUpdated 5 years ago

Dongjun Chung

Rendered from GGPA-example.Rnw in GGPA 1.19.0.
An Introduction to the REMP PackageUpdated 5 years ago

Yinan Zheng

Rendered from REMP.Rnw in REMP 1.31.0.
logicFS ManualUpdated 5 years ago

Holger Schwender

Rendered from logicFS.Rnw in logicFS 2.27.0.
The Shiny Variant ExplorerUpdated 5 years ago

Kévin Rue-Albrecht

Rendered from tSVE.Rmd in TVTB 1.33.0.
ModstringsUpdated 5 years ago

Felix G.M. Ernst & Denis L.J. Lafontaine

Rendered from Modstrings.Rmd in Modstrings 1.23.0.
Importing tRNAscan-SE output as GRangesUpdated 5 years ago

Felix G.M. Ernst

Rendered from tRNAscanImport.Rmd in tRNAscanImport 1.27.0.
gpuMagic quick start guideUpdated 5 years ago

Jiefei Wang

Rendered from Quick_start_guide.Rmd in gpuMagic 1.23.0.
maSigPro VignetteUpdated 5 years ago

Maria Jose Nueda

Rendered from maSigPro.Rnw in maSigPro 1.79.0.
INSPEcT - INference of Synthesis, Processing and dEgradation rates from Transcriptomic dataUpdated 5 years ago

de Pretis S., Furlan M., Pelizzola M.

Rendered from INSPEcT.Rmd in INSPEcT 1.37.0.
rfaRmUpdated 5 years ago

Lara Selles Vidal

Rendered from rfaRm.Rmd in rfaRm 1.19.0.
GPAUpdated 5 years ago

Dongjun Chung

Rendered from GPA-example.Rnw in GPA 1.19.0.
Global TestUpdated 5 years ago

Jelle Goeman

Rendered from GlobalTest.Rnw in globaltest 5.61.0.
Simulating and cleaning gene expression data using RUVcorr in the context of inferring gene co-expressionUpdated 5 years ago

Saskia Freytag

Rendered from Vignette.Rmd in RUVcorr 1.39.0.
Detection of differential gene expression distributions in single-cell RNA sequencing dataUpdated 5 years ago

Julian Flesch

Rendered from wasserstein_singlecell.Rmd in waddR 1.21.0.
Vignette for Dune: merging clusters to improve replicability through ARI mergingUpdated 5 years ago

Hector Roux de Bézieux

Rendered from Dune.Rmd in Dune 1.19.0.
Two-sample tests based on the 2-Wasserstein distanceUpdated 5 years ago

Julian Flesch

Rendered from wasserstein_test.Rmd in waddR 1.21.0.
2-Wasserstein distance calculationUpdated 5 years ago

Julian Flesch

Rendered from wasserstein_metric.Rmd in waddR 1.21.0.
Basic Functions for Flow Cytometry DataUpdated 5 years ago

Mike Jiang

Rendered from ncdfFlow.Rnw in ncdfFlow 2.53.0.
MSstatsQCgui: A shiny app for longitudinal quality monitoring for proteomic experimentsUpdated 5 years ago

Eralp DOGU [email protected], Sara TAHERI [email protected], Olga VITEK [email protected]

Rendered from MSstatsQCgui.Rmd in MSstatsQCgui 1.27.0.
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – Advanced usageUpdated 5 years ago

Kathleen Zeglinski, Arthur Hsu, Constantinos Koutsakis, Monther Alhamdoosh

Rendered from gmoviz_advanced.Rmd in gmoviz 1.19.0.
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – An overviewUpdated 5 years ago

Kathleen Zeglinski, Arthur Hsu, Constantinos Koutsakis, Monther Alhamdoosh

Rendered from gmoviz_overview.Rmd in gmoviz 1.19.0.
Spatial transcriptomics cluster analysis with SpatialCPieUpdated 5 years ago

Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg

Rendered from SpatialCPie.Rmd in SpatialCPie 1.23.0.
CFAssayUpdated 5 years ago

Herbert Braselmann

Rendered from cfassay.Rnw in CFAssay 1.41.0.
annotationTools: OverviewUpdated 5 years ago

Alexandre Kuhn

Rendered from annotationTools.Rnw in annotationTools 1.81.0.
Identify reproducible genomic interactions from replicate ChIA-PET experimentsUpdated 5 years ago

Konstantin Krismer

Rendered from idr2d.Rmd in idr2d 1.21.0.
Identify reproducible genomic peaks from replicate ChIP-seq experimentsUpdated 5 years ago

Konstantin Krismer

Rendered from idr1d.Rmd in idr2d 1.21.0.
Introduction to EBImageUpdated 5 years ago

Andrzej Oleś, Gregoire Pau, Oleg Sklyar, Wolfgang Huber

Rendered from EBImage-introduction.Rmd in EBImage 4.49.0.
Generating reference files for spliced and unspliced abundance estimation with alignment-free methodsUpdated 5 years ago

Charlotte Soneson

Rendered from rna-velocity.Rmd in eisaR 1.19.0.
GEOsubmission OverviewUpdated 5 years ago

Alexandre Kuhn

Rendered from GEOsubmission.Rnw in GEOsubmission 1.59.0.
Creating Your Docker Container and Command Line Interface (with docopt)Updated 5 years ago

Phil Webster

Rendered from docker.Rmd in sevenbridges 1.37.0.
Find Data on CGC via Data Browser and Datasets APIUpdated 5 years ago

Phil Webster

Rendered from cgc-datasets.Rmd in sevenbridges 1.37.0.
IDE Container: RStudio Server, Shiny Server, and MoreUpdated 5 years ago

Phil Webster

Rendered from rstudio.Rmd in sevenbridges 1.37.0.
Master Tutorial: Use R for Cancer Genomics CloudUpdated 5 years ago

Phil Webster

Rendered from bioc-workflow.Rmd in sevenbridges 1.37.0.
Feature Selection and Hierarchical Clustering of cells in Zhengmix4eqUpdated 5 years ago

Tae Kim

Rendered from example.Rmd in HIPPO 1.19.0.
SCnorm VignetteUpdated 5 years ago

Rhonda Bacher

Rendered from SCnorm.Rnw in SCnorm 1.29.0.
Predicting cell cycle phase using pecoUpdated 5 years ago

Joyce Hsiao

Rendered from vignette.Rmd in peco 1.19.0.
Updating methylSig codeUpdated 5 years ago

Raymond G. Cavalcante

Rendered from updating-methylSig-code.Rmd in methylSig 1.19.0.
Using methylSigUpdated 5 years ago

Yongseok Park, Raymond G. Cavalcante, Maria E. Figueroa, Laura S. Rozek, and Maureen A. Sartor

Rendered from using-methylSig.Rmd in methylSig 1.19.0.
sva tutorialUpdated 5 years ago

Jeffrey T. Leek

Rendered from sva.Rnw in sva 3.55.0.
Using MAST with RNASeq: MAIT Analysis.Updated 5 years ago

Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex Shalek, Chloe K. Schlicter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter Linsley, Raphael Gottardo

Rendered from MAITAnalysis.Rmd in MAST 1.33.0.
a workflow of cogenaUpdated 5 years ago

Zhilong Jia, Michael R. Barnes

Rendered from cogena-vignette_pdf.Rmd in cogena 1.41.0.
cogena, a workflow for gene set enrichment analysis of co-expressed genesUpdated 5 years ago

Zhilong Jia, Michael R. Barnes

Rendered from cogena-vignette_html.Rmd in cogena 1.41.0.
Automatic Statistical Identification in Complex Spectra (ASICS)Updated 5 years ago

Gaëlle Lefort, Rémi Servien and Nathalie Vialaneix

Rendered from ASICS.Rmd in ASICS 2.23.0.
Using pRoloc for spatial proteomics data analysisUpdated 5 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v01-pRoloc-tutorial.Rmd in pRoloc 1.47.0.
fitTimeSeries: differential abundance analysis through time or locationUpdated 5 years ago

Joseph N. Paulson

Rendered from fitTimeSeries.Rnw in metagenomeSeq 1.49.0.
OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samplesUpdated 5 years ago

Subhadeep Das

Rendered from vignettes.Rmd in OMICsPCA 1.25.0.
VanillaICE VignetteUpdated 5 years ago

Robert Scharpf

Rendered from VanillaICE.Rnw in VanillaICE 1.69.0.
SingleCellSignalRUpdated 5 years ago

Jacques Colinge Developer

Rendered from UsersGuide.Rmd in SingleCellSignalR 1.19.0.
Transcription factor binding site (TFBS) analysis with the "TFBSTools" packageUpdated 5 years ago

Ge Tan

Rendered from TFBSTools.Rmd in TFBSTools 1.45.0.
PASTUpdated 5 years ago

Adam Thrash

Rendered from past.Rmd in PAST 1.23.0.
Getting started: scHOTUpdated 5 years ago

Shila Ghazanfar

Rendered from scHOT.Rmd in scHOT 1.19.0.
The rnaseqcomp user's guideUpdated 5 years ago

| Mingxiang Teng [email protected] | Rafael A. Irizarry [email protected] | Department of Biostatistics, Dana-Farber Cancer Institute, | Harvard T.H. Chan School Public Health, Boston, MA, USA

Rendered from rnaseqcomp.Rmd in rnaseqcomp 1.37.0.
CSAR VignetteUpdated 5 years ago

Jose M Muino

Rendered from CSAR.Rnw in CSAR 1.59.0.
Gene Selection based on a mixture of marginal distributionsUpdated 5 years ago

Weiliang Qiu

Rendered from gsMMD.Rnw in GeneSelectMMD 2.51.0.
ROCpAI: ROC Partial Area Indexes for evaluating classifiersUpdated 5 years ago

Manuel Franco, Juana-María Vivo, Juan Pedro García-Ortiz

Rendered from vignettes.Rmd in ROCpAI 1.19.0.
tigre User GuideUpdated 5 years ago

Antti Honkela

Rendered from tigre.Rnw in tigre 1.61.0.
puma User GuideUpdated 5 years ago

Xuejun Liu

Rendered from puma.Rnw in puma 3.49.0.
Using the dupRadar packageUpdated 5 years ago

Sergi Sayols, Holger Klein

Rendered from dupRadar.Rmd in dupRadar 1.37.0.
Introduction To HiCBricksUpdated 5 years ago

Koustav Pal, Ilario Tagliaferri, Carmen Maria Livi

Rendered from IntroductionToHiCBricks.rmd in HiCBricks 1.25.0.
NBAMSeq: Negative Binomial Additive Model for RNA-Seq DataUpdated 5 years ago

Xu Ren and Pei Fen Kuan

Rendered from NBAMSeq-vignette.Rmd in NBAMSeq 1.23.0.
Enrichment VignetteUpdated 5 years ago

Michael T. Zimmermann

Rendered from enrichment.Rmd in RITAN 1.31.0.
Correcting FISH probe counts with frenchFISHUpdated 5 years ago

Adam Berman

Rendered from frenchFISH.Rmd in frenchFISH 1.19.0.
GmicR_vignetteUpdated 5 years ago

Richard Virgen-Slane

Rendered from GmicR_vignette.Rmd in GmicR 1.21.0.
M3C: Monte Carlo Reference-based Consensus ClusteringUpdated 5 years ago

Christopher R John

Rendered from M3Cvignette.Rmd in M3C 1.29.0.
AW Fisher tutorialUpdated 5 years ago

Zhiguang Huo (Department of Biostatistics, University of Florida)

Rendered from AWFisher.Rmd in AWFisher 1.21.0.
User manualUpdated 5 years ago

Dongmin Jung

Rendered from PPInfer.Rnw in PPInfer 1.33.0.
INSPEcT-GUIUpdated 5 years ago

de Pretis S., Furlan M., Pelizzola M.

Rendered from INSPEcT_GUI.rmd in INSPEcT 1.37.0.
ModDNAString alphabetUpdated 5 years ago

Felix G.M. Ernst & Denis L.J. Lafontaine

Rendered from ModDNAString-alphabet.Rmd in Modstrings 1.23.0.
ModRNAString alphabetUpdated 5 years ago

Felix G.M. Ernst & Denis L.J. Lafontaine

Rendered from ModRNAString-alphabet.Rmd in Modstrings 1.23.0.
SurvComp: a package for performance assessment and comparison for survival analysisUpdated 5 years ago

Benjamin Haibe-Kains

Rendered from survcomp.Rnw in survcomp 1.57.0.
Vulcan: VirtUaL ChIP-Seq Analysis through NetworksUpdated 5 years ago

Federico M. Giorgi

Rendered from vulcan.Rnw in vulcan 1.29.0.
RNAmodR.ML: detecting patterns of post-transcriptional modifications using machine learningUpdated 5 years ago

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered from RNAmodR.ML.Rmd in RNAmodR.ML 1.21.0.
Mapping between genome, transcript and protein coordinatesUpdated 5 years ago

Johannes Rainer

Rendered from coordinate-mapping.Rmd in ensembldb 2.31.0.
ERSSA Package IntroductionUpdated 5 years ago

Zixuan Shao

Rendered from ERSSA.Rmd in ERSSA 1.25.0.
Analyzing tRNA sequences and structuresUpdated 5 years ago

Felix G.M. Ernst

Rendered from tRNA.Rmd in tRNA 1.25.0.
StructstringsUpdated 5 years ago

Felix G.M. Ernst

Rendered from Structstrings.Rmd in Structstrings 1.23.1.
PICS: Probabilistic Inference for ChIP-SeqUpdated 5 years ago

Renan Sauteraud

Rendered from PICS.Rmd in PICS 2.51.0.
microbiomeDASimUpdated 5 years ago

Justin Williams

Rendered from microbiomeDASim.Rnw in microbiomeDASim 1.21.0.
mBPCRUpdated 5 years ago

P.M.V. Rancoita

Rendered from mBPCR.Rnw in mBPCR 1.61.0.
RNAmodR: RiboMethSeqUpdated 5 years ago

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered from RNAmodR.RiboMethSeq.Rmd in RNAmodR.RiboMethSeq 1.21.0.
RNAmodR: AlkAnilineSeqUpdated 5 years ago

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered from RNAmodR.AlkAnilineSeq.Rmd in RNAmodR.AlkAnilineSeq 1.21.0.
oligo User's GuideUpdated 5 years ago

Benilton Carvalho

Rendered from oug.Rnw in oligo 1.71.0.
ncGTW User ManualUpdated 5 years ago

Chiung-Ting Wu

Rendered from ncGTW.Rmd in ncGTW 1.21.0.
Analysing thermal proteome profiling data with the NPARC packageUpdated 5 years ago

Dorothee Childs, Nils Kurzawa

Rendered from NPARC.Rmd in NPARC 1.19.0.
clstUpdated 5 years ago

Noah Hoffman

Rendered from pplacerDemo.Rnw in clstutils 1.55.0.
clstutilsUpdated 5 years ago

Noah Hoffman

Rendered from refSet.Rnw in clstutils 1.55.0.
clstUpdated 5 years ago

Noah Hoffman

Rendered from clstDemo.Rnw in clst 1.55.0.
Primer Updated 5 years ago

Reid F. Thompson

Rendered from MassArray.Rnw in MassArray 1.59.0.
PLPE OverviewUpdated 5 years ago

Soo-heang Eo

Rendered from PLPE.Rnw in PLPE 1.67.0.
OverviewUpdated 5 years ago

Soo-heang Eo

Rendered from rbsurv.Rnw in rbsurv 2.65.0.
xmapbridge primerUpdated 5 years ago

Chris Wirth

Rendered from xmapbridge.Rnw in xmapbridge 1.65.0.
affy contamination toolsUpdated 5 years ago

V. Carey

Rendered from affyContam.Rnw in affyContam 1.65.0.
Using the DMR Scan PackageUpdated 5 years ago

Christian M Page

Rendered from DMRScan_vignette.Rmd in DMRScan 1.29.0.
An introduction to rScudoUpdated 5 years ago

Matteo Ciciani, Thomas Cantore, Mario Lauria

Rendered from rScudo-vignette.Rmd in rScudo 1.23.0.
esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysisUpdated 5 years ago

Zheng Wei and Wei Zhang

Rendered from esATAC-Introduction.Rmd in esATAC 1.29.0.
Manual for the phenoTest libraryUpdated 5 years ago

Evarist Planet

Rendered from phenoTest.Rnw in phenoTest 1.55.0.
The rGADEM users guideUpdated 5 years ago

Arnaud Droit

Rendered from rGADEM.Rnw in rGADEM 2.55.0.
Componentized Pipeline FrameworkUpdated 5 years ago

Zheng Wei and Shining Ma

Rendered from pipeFrame.Rmd in pipeFrame 1.23.0.
Introduction to netSmooth packageUpdated 5 years ago

Jonathan Ronen, Altuna Akalin

Rendered from netSmoothIntro.Rmd in netSmooth 1.27.0.
topGOUpdated 5 years ago

Adrian Alexa

Rendered from topGO.Rnw in topGO 2.59.0.
Introduction to the scFeatureFilter packageUpdated 5 years ago

Angeles Arzalluz-Luque, Guillaume Devailly, Anagha Joshi

Rendered from Introduction.Rmd in scFeatureFilter 1.27.0.
Application of PepsNMR on the Human Serum datasetUpdated 5 years ago

Manon Martin

Rendered from PepsNMR_minimal_example.Rmd in PepsNMR 1.25.0.
Probability plot usageUpdated 5 years ago

Jakob Theorell

Rendered from GroupProbPlot_usage.Rmd in DepecheR 1.23.0.
ChIP-seq signal quantifier (CSSQ)Updated 5 years ago

Ashwath Kumar, Yajun Mei, Yuhong Fan

Rendered from CSSQ.Rmd in CSSQ 1.19.0.
Statistical analysis and visualization of functional profiles for genes and gene clustersUpdated 5 years ago

Guangchuang Yu

Rendered from clusterProfiler.Rmd in clusterProfiler 4.15.0.
consensusDE: DE analysis using multiple algorithmsUpdated 5 years ago

Ashley J. Waardenberg

Rendered from consensusDE.Rmd in consensusDE 1.25.0.
Atom count expectations with compoundQuantilesUpdated 5 years ago

Steffen Neumann

Rendered from compoundQuantilesVignette.Rnw in CAMERA 1.63.0.
regsplice workflowUpdated 5 years ago

Lukas M. Weber, Mark D. Robinson

Rendered from regsplice-workflow.Rmd in regsplice 1.33.0.
flowStats OverviewUpdated 5 years ago

Greg Finak

Rendered from GettingStartedWithFlowStats.Rnw in flowStats 4.19.0.
A TCGA dataset applicationUpdated 5 years ago

Selcen Ari

Rendered from mirtarbase_example.Rmd in ceRNAnetsim 1.19.0.
The auxiliary commands which can help to the usersUpdated 5 years ago

Selcen Ari

Rendered from auxiliary_commands.Rmd in ceRNAnetsim 1.19.0.
Calculating Number of Iterations Required to Reach Steady-StateUpdated 5 years ago

Selcen Ari

Rendered from convenient_iteration.Rmd in ceRNAnetsim 1.19.0.
Basic Use of ceRNAnetsimUpdated 5 years ago

Selcen Ari

Rendered from basic_usage.Rmd in ceRNAnetsim 1.19.0.
Fragmentation Analysis with topdownrUpdated 5 years ago

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered from analysis.Rmd in topdownr 1.29.0.
Splicing graphs and RNA-seq dataUpdated 5 years ago

H. Pagès

Rendered from SplicingGraphs.Rnw in SplicingGraphs 1.47.0.
A walkthrough the easyRNASeq package functionalitiesUpdated 5 years ago

Nicolas Delhomme

Rendered from simpleRNASeq.Rmd in easyRNASeq 2.43.0.
R / Bioconductor for High Throughput Sequence AnalysisUpdated 5 years ago

Nicolas Delhomme

Rendered from easyRNASeq.Rnw in easyRNASeq 2.43.0.
Using RProtoBufLibUpdated 5 years ago

Mike Jiang

Rendered from UsingRProtoBufLib.Rmd in RProtoBufLib 2.19.0.
Trendy VignetteUpdated 5 years ago

Rhonda Bacher

Rendered from Trendy_vignette.Rnw in Trendy 1.29.0.
RTNduals: analysis of co-regulation and inference of dual regulons.Updated 5 years ago

Vinicius S. Chagas, Clarice S. Groeneveld, Kerstin B. Meyer, A. Gordon Robertson, Mauro A. A. Castro.

Rendered from RTNduals.Rmd in RTNduals 1.31.0.
How to write a csv gating templateUpdated 5 years ago

Mike Jiang

Rendered from HowToWriteCSVTemplate.Rmd in openCyto 2.19.0.
Using Chromosome Bands as CategoriesUpdated 5 years ago

Bioconductor Package Maintainer

Rendered from ChromBand.Rnw in Category 2.73.0.
metagene2: a package to produce metagene plotsUpdated 5 years ago

Eric Fournier

Rendered from metagene2.Rmd in metagene2 1.23.0.
Extending dispatch to more batch correction methodsUpdated 5 years ago

Aaron Lun

Rendered from extension.Rmd in batchelor 1.23.0.
selectKSigs: a package for selecting the number of mutational signaturesUpdated 5 years ago

Zhi Yang

Rendered from selectKSigs.Rmd in selectKSigs 1.19.0.
Using HDTD to Analyze High-Dimensional Transposable Data: An Application in GeneticsUpdated 5 years ago

Touloumis, A., Marioni, J.C., and Tavaré, S.

Rendered from HDTD.Rmd in HDTD 1.41.0.
Notes on ROC packageUpdated 5 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from ROCnotes.Rmd in ROC 1.83.0.
debCAM User ManualUpdated 5 years ago

Lulu Chen

Rendered from debcam.Rmd in debCAM 1.25.0.
Getting Started with Methylation-based Inference of Regulatory ActivityUpdated 5 years ago

John Lawson

Rendered from GettingStarted.Rmd in MIRA 1.29.0.
Ularcirc: A shiny application for canonical and back splicing analysisUpdated 5 years ago

David Humphreys, Nicolas Fossat, Patrick Tam, Joshua Ho

Rendered from Ularcirc.Rmd in Ularcirc 1.25.0.
Building PPIs from StringDBUpdated 5 years ago

Jonathan Ronen, Altuna Akalin

Rendered from buildingPPIsFromStringDB.Rmd in netSmooth 1.27.0.
Explore data integration and batch effectsUpdated 5 years ago

Almut Luetge, Mark D Robinson

Rendered from CellMixS.Rmd in CellMixS 1.23.0.
MACSQuantifyR - Step-by-step analysisUpdated 5 years ago

Raphaël Bonnet, Jean-François Peyron

Rendered from MACSQuantifyR_combo.Rmd in MACSQuantifyR 1.21.0.
RNAsenseUpdated 5 years ago

Marcus Rosenblatt

Rendered from example.Rmd in RNAsense 1.21.0.
Link-HD: a versatile framework to explore and integrate heterogeneous dataUpdated 5 years ago

Laura M Zingaretti, Yuliaxis Ramayo-Caldas

Rendered from LinkHD.Rmd in LinkHD 1.21.0.
AffiXcanUpdated 5 years ago

Alessandro Lussana

Rendered from AffiXcan.Rmd in AffiXcan 1.25.0.
TPP_introduction_NPARCUpdated 5 years ago

Dorothee Childs

Rendered from NPARC_analysis_of_TPP_TR_data.Rnw in TPP 3.35.0.
Outlier Analysis using blacksheeprUpdated 5 years ago

MacIntosh Cornwell

Rendered from blacksheepr_vignette.Rmd in blacksheepr 1.21.0.
MACSQuantifyR - IntroductionUpdated 5 years ago

Raphaël Bonnet, Jean-François Peyron

Rendered from MACSQuantifyR.Rmd in MACSQuantifyR 1.21.0.
MACSQuantifyR - Automatic pipelineUpdated 5 years ago

Raphaël Bonnet, Jean-François Peyron

Rendered from MACSQuantifyR_pipeline.Rmd in MACSQuantifyR 1.21.0.
lionessRUpdated 5 years ago

Marieke L. Kuijjer

Rendered from lionessR.Rmd in lionessR 1.21.0.
RNAmodR: creating classes for additional modification detection from high throughput sequencing.Updated 5 years ago

Felix G.M. Ernst

Rendered from RNAmodR.creation.Rmd in RNAmodR 1.21.0.
BrowserViz: A base class providing simple, extensible message passing between your R session and web browser, for interactive data visualization.Updated 5 years ago

Paul Shannon

Rendered from BrowserViz.Rmd in BrowserViz 2.29.0.
INDEED R package for cancer biomarker discoveryUpdated 5 years ago

Yiming Zuo and Kian Ghaffari

Rendered from Introduction_to_INDEED.Rmd in INDEED 2.21.0.
Using target to predict combined bindingUpdated 5 years ago

Mahmoud Ahmed

Rendered from extend-target.Rmd in target 1.21.0.
Triplex User GuideUpdated 5 years ago

Jiri Hon

Rendered from triplex.Rnw in triplex 1.47.0.
TissueEnrich: A tool to calculate tissue-specific gene enrichmentUpdated 5 years ago

| Ashish Jain, Geetu Tuteja | Bioinformatics and Computational Biology | Genetics, Development, and Cell Biology | Iowa State University, Ames, Iowa |

Rendered from TissueEnrich.Rmd in TissueEnrich 1.27.0.
MAST IntroUpdated 5 years ago

Andrew McDavid, Greg Finak

Rendered from MAST-Intro.Rmd in MAST 1.33.0.
Delta Capure-CUpdated 5 years ago

Michael Shapiro

Rendered from deltaCaptureC.Rmd in deltaCaptureC 1.21.0.
Description of Encrypted IDAT FormatUpdated 5 years ago

Kasper Daniel Hansen

Rendered from EncryptedFormat.Rnw in illuminaio 0.49.0.
Introduction to illuminaioUpdated 5 years ago

Kasper Daniel Hansen

Rendered from illuminaio.Rnw in illuminaio 0.49.0.
Using the target packageUpdated 5 years ago

Mahmoud Ahmed

Rendered from target.Rmd in target 1.21.0.
Introduction to calmUpdated 5 years ago

Kun Liang

Rendered from calm_intro.Rmd in calm 1.21.0.
NADfinder GuideUpdated 5 years ago

Jianhong Ou, Haibo Liu, Jun Yu, Paul Kaufman and Lihua Julie Zhu

Rendered from NADfinder.Rmd in NADfinder 1.31.0.
Introduction to SigsPackUpdated 5 years ago

Franziska Schumann

Rendered from SigsPack.Rmd in SigsPack 1.21.0.
panelcn.mops: Manual for the R packageUpdated 5 years ago

Gundula Povysil

Rendered from panelcn.mops.Rnw in panelcn.mops 1.29.0.
Writing WrappersUpdated 5 years ago

Shian Su

Rendered from WritingWrappers.Rmd in CellBench 1.23.0.
Gene Detection Analysis for scRNA-seqUpdated 5 years ago

Ruoxin Li, Gerald Quon

Rendered from vignette.Rmd in scBFA 1.21.0.
Evaluating differential co-expression methods using dcanrUpdated 5 years ago

Dharmesh D Bhuva

Rendered from dcanr_evaluation_vignette.Rmd in dcanr 1.23.0.
Proteomics Data ImportUpdated 5 years ago

Constantin Ahlmann-Eltze

Rendered from data-import.Rmd in proDA 1.21.0.
IntroductionUpdated 5 years ago

Constantin Ahlmann-Eltze

Rendered from Introduction.Rmd in proDA 1.21.0.
How to use breakpointRUpdated 5 years ago

David Porubsky

Rendered from breakpointR.Rnw in breakpointR 1.25.0.
Introduction to qckitfastqUpdated 5 years ago

August Guang and Wenyue Xing

Rendered from vignette-qckitfastq.Rmd in qckitfastq 1.23.0.
regioneR: Association analysis of genomic regions based on permutation testsUpdated 5 years ago

Bernat Gel ([email protected]), Anna Diez-Villanueva ([email protected]) and Roberto Malinverni ([email protected])

Rendered from regioneR.Rmd in regioneR 1.39.0.
ViDGER Supplementary MaterialUpdated 5 years ago

Brandon Monier, Adam McDermaid, Jing Zhao, Qin Ma

Rendered from vidger.Rmd in vidger 1.27.0.
ccfindR: single-cell RNA-seq analysis using Bayesian non-negative matrix factorizationUpdated 5 years ago

Jun Woo, Constantin Aliferis, Jinhua Wang

Rendered from ccfindR.Rmd in ccfindR 1.27.0.
A guide to the GEMINI R packageUpdated 5 years ago

Mahdi Zamanighomi and Sidharth Jain

Rendered from gemini-quickstart.Rmd in gemini 1.21.0.
SCANVISUpdated 5 years ago

Phaedra Agius

Rendered from runningSCANVIS.Rnw in SCANVIS 1.21.0.
Transcription Factor Association Rule MinerUpdated 5 years ago

Liuba Nausicaa Martino

Rendered from TFARM.Rnw in TFARM 1.29.0.
HiLDA: a package for testing the burdens of mutational signaturesUpdated 5 years ago

Zhi Yang

Rendered from HiLDA.Rmd in HiLDA 1.21.0.
Vignette illustrating the use of graper in logistic regressionUpdated 5 years ago

Britta Velten

Rendered from example_logistic.Rmd in graper 1.23.0.
seqCAT: The High Throughput Sequencing Cell Authentication ToolkitUpdated 5 years ago

Erik Fasterius

Rendered from seqCAT.Rmd in seqCAT 1.29.0.
Getting Started with LOLAUpdated 5 years ago

Nathan Sheffield

Rendered from gettingStarted.Rmd in LOLA 1.37.0.
tenXplore: ontology for scRNA-seq, applied to 10x 1.3 million neuronsUpdated 5 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from tenXplore.Rmd in tenXplore 1.29.0.
Visualizing Gates with Flow Cytometry DataUpdated 5 years ago

Mike Jiang

Rendered from filters.Rmd in flowViz 1.71.0.
Inversion genotyping with scoreInvHapUpdated 5 years ago

Carlos Ruiz-Arenas, Alejandro Caceres, Juan R. Gonzalez

Rendered from scoreInvHap.Rmd in scoreInvHap 1.29.0.
TitanCNAUpdated 5 years ago

Gavin Ha

Rendered from TitanCNA.Rnw in TitanCNA 1.45.0.
Introduction to IsoCorrectoRUpdated 6 years ago

Paul Heinrich

Rendered from IsoCorrectoRGUI.Rmd in IsoCorrectoRGUI 1.23.0.
Introduction to IsoCorrectoRUpdated 6 years ago

Paul Heinrich

Rendered from IsoCorrectoR.Rmd in IsoCorrectoR 1.25.0.
Splice event prediction and quantification from RNA-seq dataUpdated 6 years ago

Leonard D Goldstein

Rendered from SGSeq.Rmd in SGSeq 1.41.0.
moCluster: Integrative clustering using multiple omics dataUpdated 6 years ago

Chen Meng

Rendered from moCluster-knitr.Rnw in mogsa 1.41.0.
mogsa: gene set analysis on multiple omics dataUpdated 6 years ago

Chen Meng

Rendered from mogsa-knitr.Rnw in mogsa 1.41.0.
MetaNeighbor : a method to rapidly assess cell type identity using both functional and random gene setsUpdated 6 years ago

Megan Crow, Stephan Fischer, Sara Ballouz, Manthan Shah, Jesse Gillis

Rendered from MetaNeighbor.Rmd in MetaNeighbor 1.27.0.
nethetUpdated 6 years ago

Nicolas Staedler

Rendered from nethet.Rnw in nethet 1.39.0.
KinSwingR: Predicting kinase activity from phosphoproteomics dataUpdated 6 years ago

Ashley J. Waardenberg

Rendered from KinSwingR.Rmd in KinSwingR 1.25.0.
SynMut: Tools for Designing Synonymously Mutated SequencesUpdated 6 years ago

Haogao Gu, Leo L.M. Poon, School of Public Health, The University of Hong Kong

Rendered from SynMut.Rmd in SynMut 1.23.0.
Gene Set Enrichment Analysis with NetworksUpdated 6 years ago

Dongmin Jung

Rendered from gsean.Rmd in gsean 1.27.0.
SWATH2stats package VignetteUpdated 6 years ago

Peter Blattmann

Rendered from SWATH2stats_vignette.Rnw in SWATH2stats 1.37.0.
scRecoverUpdated 6 years ago

Zhun Miao, Xuegong Zhang

Rendered from scRecover.Rmd in scRecover 1.23.0.
Introduction to epivizr: interactive visualization for genomic dataUpdated 6 years ago

Héctor Corrada Bravo

Rendered from IntroToEpivizr.Rmd in epivizr 2.37.0.
A systems biology tool for gene regulatory circuit simulationUpdated 6 years ago

Vivek Kohar

Rendered from sRACIPE.Rmd in sRACIPE 1.23.0.
The VennDetail packageUpdated 6 years ago

Kai Guo, Brett McGregor, James Porter, and Junguk Hur

Rendered from VennDetail.Rmd in VennDetail 1.23.0.
GuitarUpdated 6 years ago

Jia Meng

Rendered from Guitar-Overview.Rnw in Guitar 2.23.0.
RepViz-vignetteUpdated 6 years ago

Thomas Faux, Kalle Rytkönen, Asta Laiho, Laura L. Elo

Rendered from RepViz.Rmd in RepViz 1.23.0.
Tutorial for swfdr packageUpdated 6 years ago

Jeff Leek, Simina Boca

Rendered from swfdrTutorial.Rmd in swfdr 1.33.0.
AdductomicsR workflowUpdated 6 years ago

Josie Hayes

Rendered from adductomicsRWorkflow.Rmd in adductomicsR 1.23.0.
Performing differential co-expression analysis using dcanrUpdated 6 years ago

Dharmesh D Bhuva

Rendered from dcanr_vignette.Rmd in dcanr 1.23.0.
ClusterJudgeUpdated 6 years ago

Adrian Pasculescu

Rendered from ClusterJudge-intro.Rmd in ClusterJudge 1.29.0.
Celaref ManualUpdated 6 years ago

Sarah Williams

Rendered from celaref_doco.Rmd in celaref 1.25.0.
Suppl. Ch. 1 - Quickstart Guide for New R UsersUpdated 6 years ago

Gabriel Odom

Rendered from Supplement1-Quickstart_Guide.Rmd in pathwayPCA 1.23.0.
Suppl. Ch. 3 - Creating Data ObjectsUpdated 6 years ago

Gabriel Odom

Rendered from Supplement3-Create_Omics_Objects.Rmd in pathwayPCA 1.23.0.
Suppl. Ch. 4 - Test Pathway SignificanceUpdated 6 years ago

Gabriel Odom

Rendered from Supplement4-Methods_Walkthrough.Rmd in pathwayPCA 1.23.0.
Annotating spatial proteomics dataUpdated 6 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v04-pRoloc-goannotations.Rmd in pRoloc 1.47.0.
Iterators in SeqVarToolsUpdated 6 years ago

Stephanie M. Gogarten

Rendered from Iterators.Rnw in SeqVarTools 1.45.0.
Bayesian Analysis of Spatial Proteomics data using pRolocUpdated 6 years ago

Oliver Crook, Laurent Gatto

Rendered from v03-pRoloc-bayesian.Rmd in pRoloc 1.47.0.
Singular value decomposition for Bioconductor packagesUpdated 6 years ago

Aaron Lun

Rendered from decomposition.Rmd in BiocSingular 1.23.0.
BiGGRUpdated 6 years ago

Anand K. Gavai

Rendered from BiGGR.Rnw in BiGGR 1.43.0.
Merging Mixture Components for Cell Population Identification in Flow Cytometry Data The flowMerge packageUpdated 6 years ago

Greg Finak, Raphael Gottardo

Rendered from flowmerge.Rmd in flowMerge 2.55.0.
Customized opencl codeUpdated 6 years ago

Jiefei Wang

Rendered from Customized-openCL-code.Rmd in gpuMagic 1.23.0.
flowPloidy: Getting StartedUpdated 6 years ago

Tyler Smith

Rendered from flowPloidy-gettingStarted.Rmd in flowPloidy 1.33.0.
The RVS (Rare Variant Sharing) PackageUpdated 6 years ago

Alexandre Bureau, Ingo Ruczinski, Samuel Younkin, Thomas Sherman

Rendered from RVS.Rmd in RVS 1.29.0.
Workflow for NetPathMinerUpdated 6 years ago

Ahmed Mohamed

Rendered from NPMVignette.Rmd in NetPathMiner 1.43.0.
diffcyt workflowUpdated 6 years ago

Lukas M. Weber, Malgorzata Nowicka, Charlotte Soneson, Mark. D. Robinson

Rendered from diffcyt_workflow.Rmd in diffcyt 1.27.0.
Case study: predicting protein functionUpdated 6 years ago

Sergio Picart-Armada

Rendered from diffuStats.Rnw in diffuStats 1.27.0.
vignette-hierinf.RnwUpdated 6 years ago

Claude Renaux

Rendered from vignette-hierinf.Rnw in hierinf 1.25.0.
Introduction to bayNormUpdated 6 years ago

Wenhao Tang, Fran<U+00E7>ois Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei

Rendered from bayNorm.Rmd in bayNorm 1.25.0.
ssrch: selectize-based search engine for corpora of modest sizeUpdated 6 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from ssrch.Rmd in ssrch 1.23.0.
flowPloidy: Flow Cytometry HistogramsUpdated 6 years ago

Tyler Smith

Rendered from histogram-tour.Rmd in flowPloidy 1.33.0.
Subtype Identification with Survival DataUpdated 6 years ago

Dongmin Jung

Rendered from survtype.Rmd in survtype 1.23.0.
TCGAbiolinks version bump with new functionsUpdated 6 years ago

Mohamed Mounir

Rendered from extension.Rmd in TCGAbiolinks 2.35.0.
R/Bioconductor package for normalization and differential expression inference in time series gene expression microarray data.Updated 6 years ago

Dipen P. Sangurdekar

Rendered from Rnits-vignette.Rnw in Rnits 1.41.0.
chimeravizUpdated 6 years ago

Stian Lågstad

Rendered from chimeraviz-vignette.Rmd in chimeraviz 1.33.0.
Machine learning techniques available in pRolocUpdated 6 years ago

Laurent Gatto

Rendered from v02-pRoloc-ml.Rmd in pRoloc 1.47.0.
Interactome reconstruction from co-elution data with PrInCEUpdated 6 years ago

Michael Skinnider

Rendered from intro-to-prince.Rmd in PrInCE 1.23.0.
doseRUpdated 6 years ago

AJ Vaestermark, JR Walters.

Rendered from doseR.Rmd in doseR 1.23.0.
(Deprecated) How to use bimaps from the ".db" annotation packages Updated 6 years ago

Bioconductor Package Maintainer

Rendered from AnnotationDbi.Rnw in AnnotationDbi 1.69.0.
Rqc - Quality Control Tool for High-Throughput Sequencing DataUpdated 6 years ago

Welliton Souza, Benilton Carvalho

Rendered from Rqc.Rmd in Rqc 1.41.0.
Using VIPERUpdated 6 years ago

Mariano J Alvarez

Rendered from viper.Rnw in viper 1.41.0.
DEScan2Updated 6 years ago

Dario Righelli - John Koberstein - Bruce Gomes

Rendered from DEScan2.Rmd in DEScan2 1.27.0.
CGEN Scan VignetteUpdated 6 years ago

Justin Lee

Rendered from vignette_GxE.Rnw in CGEN 3.43.0.
Alternative CDF environments for 2(or more)-genomes chipsUpdated 6 years ago

Laurent Gautier

Rendered from ngenomeschips.Rnw in altcdfenvs 2.69.0.
Modifying existing CDF environments to make alternative CDF environmentsUpdated 6 years ago

Laurent Gautier

Rendered from modify.Rnw in altcdfenvs 2.69.0.
Sequence Analysis with OmaDBUpdated 6 years ago

Klara Kaleb

Rendered from sequence_mapping.Rmd in OmaDB 2.23.0.
Get started with OmaDBUpdated 6 years ago

Klara Kaleb

Rendered from OmaDB.Rmd in OmaDB 2.23.0.
Analyzing Illumina Methylation Array Data in RaMWASUpdated 6 years ago

Andrey A Shabalin

Rendered from RW5a_matrix.Rmd in ramwas 1.31.0.
Analyzing Data from Other Methylation Platforms or Data TypesUpdated 6 years ago

Andrey A Shabalin

Rendered from RW5c_matrix.Rmd in ramwas 1.31.0.
QC-free approach with Combat methodUpdated 6 years ago

Hemi Luan

Rendered from Combat.Rmd in statTarget 1.37.0.
Performing Divergence AnalysisUpdated 6 years ago

Wikum Dinalankara, Luigi Marchionni, Qian Ke

Rendered from divergence.Rmd in divergence 1.23.0.
FELLAUpdated 6 years ago

Sergio Picart-Armada

Rendered from FELLA.Rnw in FELLA 1.27.0.
SMAD Quick StartUpdated 6 years ago

Qingzhou (Johnson) Zhang

Rendered from quickstart.Rmd in SMAD 1.23.0.
Building a minimal genome browser with h5vc and shinyUpdated 6 years ago

Paul Theodor Pyl

Rendered from h5vc.simple.genome.browser.Rmd in h5vc 2.41.0.
h5vc -- TourUpdated 6 years ago

Paul Theodor Pyl

Rendered from h5vc.tour.Rmd in h5vc 2.41.0.
xina_user_codeUpdated 6 years ago

Lang Ho Lee

Rendered from xina_user_code.Rmd in XINA 1.25.0.
Timing methods in CellBenchUpdated 6 years ago

Shian Su

Rendered from Timing.Rmd in CellBench 1.23.0.
Aligning reads with Rhisat2Updated 6 years ago

Charlotte Soneson

Rendered from Rhisat2.Rmd in Rhisat2 1.23.0.
Using extract_transcripts in drawProteinsUpdated 6 years ago

Dr Paul Brennan

Rendered from drawProteins_extract_transcripts_BiocStyle.Rmd in drawProteins 1.27.0.
Using drawProteinsUpdated 6 years ago

Dr Paul Brennan

Rendered from drawProteins_BiocStyle.Rmd in drawProteins 1.27.0.
Vignette illustrating the use of graper in linear regressionUpdated 6 years ago

Britta Velten

Rendered from example_linear.Rmd in graper 1.23.0.
article frameUpdated 6 years ago

Armin Rauschenberger

Rendered from article.Rmd in semisup 1.31.0.
vignette frameUpdated 6 years ago

Armin Rauschenberger

Rendered from vignette.Rmd in semisup 1.31.0.
vignette sourceUpdated 6 years ago

Armin Rauschenberger

Rendered from semisup.Rnw in semisup 1.31.0.
An Introduction To strandCheckRUpdated 6 years ago

Thu-Hien To, Steve Pederson

Rendered from strandCheckR.Rmd in strandCheckR 1.25.0.
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seqUpdated 6 years ago

Christian Oertlin

Rendered from anota2seq.Rnw in anota2seq 1.29.0.
FABIA: Manual for the R packageUpdated 6 years ago

Andreas Mitterecker

Rendered from fabia.Rnw in fabia 2.53.0.
Introduction to PhenoPathUpdated 6 years ago

Kieran R Campbell

Rendered from introduction_to_phenopath.Rmd in phenopath 1.31.0.
PAIRADISEUpdated 6 years ago

Qiang Hu

Rendered from pairadise.Rmd in PAIRADISE 1.23.0.
pathway analysis (mummichog)Updated 6 years ago

Hemi Luan

Rendered from pathway_analysis.Rmd in statTarget 1.37.0.
CEMiTool: Co-expression Modules Identification ToolUpdated 6 years ago

Helder Nakaya

Rendered from CEMiTool.Rmd in CEMiTool 1.31.0.
OVESEG User ManualUpdated 6 years ago

Lulu Chen

Rendered from OVESEG.Rmd in OVESEG 1.23.0.
Visualization of Functional Enrichment ResultUpdated 6 years ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from enrichplot.Rmd in enrichplot 1.27.1.
scmeth VignetteUpdated 6 years ago

Divy S. Kangeyan

Rendered from my-vignette.Rmd in scmeth 1.27.0.
BubbleTree TutorialUpdated 6 years ago

Wei Zhu, Michael Kuziora, Todd Creasy, Brandon Higgs

Rendered from BubbleTree-vignette.Rmd in BubbleTree 2.37.0.
CluMSID --- Clustering of MS^2^ Spectra for Metabolite IdentificationUpdated 6 years ago

Tobias Depke

Rendered from CluMSID_tutorial.Rmd in CluMSID 1.23.0.
Exploring Hierarchical orthologous groups with OmaDBUpdated 6 years ago

Klara Kaleb

Rendered from exploring_hogs.Rmd in OmaDB 2.23.0.
Exploring Taxonomic trees with OmaDBUpdated 6 years ago

Klara Kaleb

Rendered from tree_visualisation.Rmd in OmaDB 2.23.0.
Clustering Spectra from High Resolution DI-MS/MS Data Using CluMSIDUpdated 6 years ago

Tobias Depke

Rendered from CluMSID_DI-MSMS.Rmd in CluMSID 1.23.0.
Clustering Mass Spectra from Low Resolution GC-EI-MS Data Using CluMSIDUpdated 6 years ago

Tobias Depke

Rendered from CluMSID_GC-EI-MS.Rmd in CluMSID 1.23.0.
Clustering Mass Spectra from Low Resolution LC-MS/MS Data Using CluMSIDUpdated 6 years ago

Tobias Depke

Rendered from CluMSID_lowres-LC-MSMS.Rmd in CluMSID 1.23.0.
Using CluMSID with a Publicly Available MetaboLights Data SetUpdated 6 years ago

Tobias Depke

Rendered from CluMSID_MTBLS.Rmd in CluMSID 1.23.0.
Introduction to DEPUpdated 6 years ago

Arne Smits

Rendered from DEP.Rmd in DEP 1.29.0.
Data Generation for topdownrUpdated 6 years ago

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered from data-generation.Rmd in topdownr 1.29.0.
HIREewasUpdated 6 years ago

Xiangyu Luo

Rendered from HIREewas.Rnw in HIREewas 1.25.0.
Inferring inheritance of differentially methylated changes across multiple generationsUpdated 6 years ago

Astrid Deschênes, Pascal Belleau and Arnaud Droit

Rendered from methylInheritance.Rmd in methylInheritance 1.31.0.
ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profilesUpdated 6 years ago

Tiago Chedraoui Silva [aut], Lijing Yao [aut], Simon Coetzee [aut], Nicole Gull [ctb], Houtan Noushmehr [ctb], Dennis J. Hazelett [ctb], Peggy Farnham [aut], Hui Shen [ctb], Peter Laird [ctb], De-Chen Lin[ctb], Benjamin P. Berman [aut]

Rendered from index.Rmd in ELMER 2.31.0.
Working with the GSReg packageUpdated 6 years ago

Bahman Afsari

Rendered from GSReg.Rnw in GSReg 1.41.0.
Working with the switchBox packageUpdated 6 years ago

Bahman Afsari

Rendered from switchBox.Rnw in switchBox 1.43.0.
Working with the matchBox packageUpdated 6 years ago

Luigi Marchionni

Rendered from matchBox.Rnw in matchBox 1.49.0.
The bumphunter user's guideUpdated 6 years ago

Tamilselvi Guharaj

Rendered from bumphunter.Rnw in bumphunter 1.49.0.
DrugVsDiseaseUpdated 6 years ago

j. Saez-Rodriguez

Rendered from DrugVsDisease.Rnw in DrugVsDisease 2.49.0.
Extending the SummarizedExperiment classUpdated 6 years ago

Aaron Lun

Rendered from Extensions.Rmd in SummarizedExperiment 1.37.0.
Introduction to the ASSIGN PackageUpdated 6 years ago

Ying Shen, David Jenkins, W. Evan Johnson

Rendered from ASSIGN.vignette.Rmd in ASSIGN 1.43.0.
powerTCRUpdated 6 years ago

Hillary Koch

Rendered from powerTCR.Rmd in powerTCR 1.27.0.
abseqR: reporting and data analysis functionalities for Rep-Seq datasets of antibody librariesUpdated 6 years ago

Jia Hong Fong, Monther Alhamdoosh

Rendered from abseqR.Rmd in abseqR 1.25.0.
WrenchUpdated 6 years ago

M. Senthil Kumar$^1$, Héctor Corrada Bravo$^1$, $^1$Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740.

Rendered from vignette.Rmd in Wrench 1.25.0.
Run PathoStatUpdated 6 years ago

Solaiappan Manimaran, Yue Zhao

Rendered from PathoStat-vignette.Rmd in PathoStat 1.33.0.
Codon usage (CU) analysis in RUpdated 6 years ago

Anamaria Elek

Rendered from coRdon.Rmd in coRdon 1.25.0.
Quasispecies DataUpdated 6 years ago

Guerrero-Murillo, M and Gregori, J

Rendered from QSUtils-Alignment.Rmd in QSutils 1.25.0.
Characterizing viral quasispeciesUpdated 6 years ago

Guerrero-Murillo, M and Gregori, J

Rendered from QSutils-Diversity.Rmd in QSutils 1.25.0.
Simulating Quasispecies CompositionUpdated 6 years ago

Guerrero-Murillo, M and Gregori, J

Rendered from QSutils-Simulation.Rmd in QSutils 1.25.0.
NOISeq User's GuideUpdated 6 years ago

Sonia Tarazona

Rendered from NOISeq.Rnw in NOISeq 2.51.0.
The bigmelon PackageUpdated 6 years ago

Leonard C. Schalkwyk

Rendered from bigmelon.Rnw in bigmelon 1.33.0.
iClusterPlusUpdated 6 years ago

Qianxing Mo

Rendered from iClusterPlus.Rnw in iClusterPlus 1.43.1.
ProteoMM - Multi-Dataset Model-based Differential Expression Proteomics PlatformUpdated 6 years ago

Yuliya V Karpievitch, Tim Stuart, Sufyaan Mohamed

Rendered from ProteoMM_vignette.Rmd in ProteoMM 1.25.0.
gwasurvivr VignetteUpdated 6 years ago

Abbas Rizvi, Ezgi Karaesmen, Martin Morgan, Lara Sucheston-Campbell

Rendered from gwasurvivr_Introduction.Rmd in gwasurvivr 1.25.0.
ExCluster VignetteUpdated 6 years ago

R. Matthew Tanner

Rendered from ExCluster.Rnw in ExCluster 1.25.0.
Simulating Whole-Genome Inherited Bisulphite Sequencing DataUpdated 6 years ago

Pascal Belleau, Astrid Deschênes and Arnaud Droit

Rendered from methInheritSim.Rmd in methInheritSim 1.29.0.
Data formats in GWASToolsUpdated 6 years ago

Stephanie M. Gogarten

Rendered from Formats.Rnw in GWASTools 1.53.0.
GWAS Data CleaningUpdated 6 years ago

Stephanie M. Gogarten

Rendered from DataCleaning.Rnw in GWASTools 1.53.0.
iChipUpdated 6 years ago

Qianxing Mo

Rendered from iChip.Rnw in iChip 1.61.0.
iSeqUpdated 6 years ago

Qianxing Mo

Rendered from iSeq.Rnw in iSeq 1.59.0.
A fatty liver study on Mus musculusUpdated 6 years ago

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered from musmusculus.Rmd in FELLA 1.27.0.
An oxybenzone exposition study on gilt-head breamUpdated 6 years ago

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered from zebrafish.Rmd in FELLA 1.27.0.
runibic: UniBic in R TutorialUpdated 6 years ago

Patryk Orzechowski, Artur Pańszczyk

Rendered from runibic.Rmd in runibic 1.29.0.
MSstatsQC: longitudinal system suitability monitoring and quality control for proteomic experimentsUpdated 6 years ago

Eralp DOGU [email protected], Sara TAHERI [email protected], Olga VITEK [email protected]

Rendered from MSstatsQC.Rmd in MSstatsQC 2.25.0.
GateFinderUpdated 6 years ago

Nima Aghaeepour

Rendered from GateFinder.Rnw in GateFinder 1.27.0.
Analyzing WGBS data with bsseqUpdated 6 years ago

Kasper Daniel Hansen

Rendered from bsseq_analysis.Rmd in bsseq 1.43.0.
The bsseq User's GuideUpdated 6 years ago

Kasper Daniel Hansen

Rendered from bsseq.Rmd in bsseq 1.43.0.
plotGrouperUpdated 6 years ago

John D. Gagnon

Rendered from plotGrouper-vignette.Rmd in plotGrouper 1.25.0.
PREDA S4-classesUpdated 6 years ago

Francesco Ferrari

Rendered from PREDAclasses.Rnw in PREDA 1.53.0.
PREDA tutorialUpdated 6 years ago

Francesco Ferrari

Rendered from PREDAtutorial.Rnw in PREDA 1.53.0.
stageR: stage-wise analysis of high-throughput gene expression data in RUpdated 6 years ago

Koen Van den Berge and Lieven Clement

Rendered from stageRVignette.Rmd in stageR 1.29.0.
Prediction of chromatin looping interactions with sevenCUpdated 6 years ago

Jonas Ibn-Salem, Miguel Andrade-Navarro

Rendered from sevenC.Rmd in sevenC 1.27.0.
Using SemDistUpdated 6 years ago

Ian Gonzalez

Rendered from introduction.rnw in SemDist 1.41.0.
PhenStat VignetteUpdated 6 years ago

Hamed Haselimashhadi

Rendered from PhenStat.Rnw in PhenStat 2.43.0.
primirTSSUpdated 6 years ago

Pumin Li

Rendered from primirTSS.Rmd in primirTSS 1.25.0.
Introduction to IWTomicsUpdated 6 years ago

Marzia A Cremona

Rendered from IWTomics.Rnw in IWTomics 1.31.0.
PathNetUpdated 6 years ago

Ludwig Geistlinger

Rendered from PathNet.Rnw in PathNet 1.47.0.
MWASToolsUpdated 6 years ago

Andrea Rodriguez-Martinez

Rendered from MWASTools.Rmd in MWASTools 1.31.0.
Visualising very long data vectors with the Hilbert curveUpdated 6 years ago

Simon Anders

Rendered from HilbertVis.Rnw in HilbertVis 1.65.0.
BAGS: A Bayesian Approach for Geneset Selection.Updated 6 years ago

Alejandro Quiroz-Zarate

Rendered from BAGS.Rnw in BAGS 2.47.0.
VegaMCUpdated 6 years ago

Sandro Morganella

Rendered from VegaMC.Rnw in VegaMC 3.45.0.
GeneBreakUpdated 6 years ago

Evert van den Broek

Rendered from GeneBreak.Rnw in GeneBreak 1.37.0.
Tutorial of flowPeaks packageUpdated 6 years ago

Yongchao Ge

Rendered from flowPeaks-guide.Rnw in flowPeaks 1.53.2.
dye bias correctionUpdated 6 years ago

Philip Lijnzaad

Rendered from dyebias-vignette.Rnw in dyebias 1.67.0.
Introduction to CytoDxUpdated 6 years ago

Zicheng Hu

Rendered from CytoDx_Vignette.Rmd in CytoDx 1.27.0.
TFutils: Data Structures for Transcription Factor BioinformaticsUpdated 6 years ago

BJ Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin Raby, Vincent Carey

Rendered from TFutils.Rmd in TFutils 1.27.1.
r Biocpkg("flowcatchR"): A framework for tracking and analyzing flowing blood cells in time lapse microscopy imagesUpdated 6 years ago

Federico Marini, Johanna Mazur, Harald Binder

Rendered from flowcatchr_vignette.Rmd in flowcatchR 1.41.0.
YARN: Robust Multi-Tissue RNA-Seq Preprocessing and NormalizationUpdated 6 years ago

Joseph N. Paulson & John Quackenbush

Rendered from yarn.Rmd in yarn 1.33.0.
Introduction to TnTUpdated 6 years ago

Jialin Ma

Rendered from introduction.Rmd in TnT 1.29.0.
TimeScape vignetteUpdated 6 years ago

Maia Smith

Rendered from timescape_vignette.Rmd in timescape 1.31.0.
ssvizUpdated 6 years ago

Diana Low

Rendered from ssviz.Rnw in ssviz 1.41.0.
An Introduction to the skewr PackageUpdated 6 years ago

Ryan Putney

Rendered from skewr.Rnw in skewr 1.39.0.
Sample Quality Check for NGS Data using SeqSQC packageUpdated 6 years ago

Qian Liu, Qianqian Zhu

Rendered from vignette.Rmd in SeqSQC 1.29.0.
sampleClassifier VignetteUpdated 6 years ago

Khadija El Amrani

Rendered from sampleClassifier.Rnw in sampleClassifier 1.31.0.
RIVERUpdated 6 years ago

Yungil Kim

Rendered from RIVER.Rmd in RIVER 1.31.0.
Multi-Tissue AnalysisUpdated 6 years ago

Michael T. Zimmermann

Rendered from multi_tissue_analysis.Rmd in RITAN 1.31.0.
RBMUpdated 6 years ago

Dongmei Li

Rendered from RBM.Rnw in RBM 1.39.0.
RaMWAS OverviewUpdated 6 years ago

Andrey A Shabalin

Rendered from RW1_intro.Rmd in ramwas 1.31.0.
Running qusageUpdated 6 years ago

Christopher Bolen

Rendered from qusage.Rnw in qusage 2.41.0.
Batch effect estimation in Microarray dataUpdated 6 years ago

Jianying LI

Rendered from pvca.Rnw in pvca 1.47.0.
The proteinProfiles packageUpdated 6 years ago

Julian Gehring

Rendered from proteinProfiles.Rnw in proteinProfiles 1.47.0.
phosphonormalizer: Pairwise normalization of phosphoproteomics dataUpdated 6 years ago

Sohrab Saraei, Tomi Suomi, Otto Kauko,Laura L. Elo

Rendered from vignette.Rmd in phosphonormalizer 1.31.0.
phosphonormalizer: Phosphoproteomics NormalizationUpdated 6 years ago

Sohrab Saraei

Rendered from phosphonormalizer.Rnw in phosphonormalizer 1.31.0.
PAA tutorialUpdated 6 years ago

Michael Turewicz

Rendered from PAA_vignette.Rnw in PAA 1.41.0.
Introduction to OPWeightUpdated 6 years ago

Mohamad S. Hasan and Paul Schliekelman

Rendered from OPWeight.Rmd in OPWeight 1.29.0.
missRowsUpdated 6 years ago

Gonzalez Ignacio

Rendered from missRows.Rnw in missRows 1.27.0.
miRNAtapUpdated 6 years ago

T. Ian Simpson

Rendered from miRNAtap.Rnw in miRNAtap 1.41.0.
methylMnMUpdated 6 years ago

Yan Zhou

Rendered from methylMnM.Rnw in methylMnM 1.45.0.
MethylMixUpdated 6 years ago

| Olivier Gevaert | | Stanford Center for Biomedical Informatics | Department of Medicine | 1265 Welch Road | Stanford CA, 94305-5479

Rendered from vignettes.Rmd in MethylMix 2.37.0.
MEDIPSUpdated 6 years ago

Lukas Chavez

Rendered from MEDIPS.Rnw in MEDIPS 1.59.0.
MapScape vignetteUpdated 6 years ago

Maia Smith

Rendered from mapscape_vignette.Rmd in mapscape 1.31.0.
isobar package for iTRAQ and TMT protein quantificationUpdated 6 years ago

Florian P Breitwieser

Rendered from isobar.Rnw in isobar 1.53.0.
IMAS : Integrative analysis of Multi-omics data for Alternative SplicingUpdated 6 years ago

Seonggyun Han

Rendered from IMAS.Rnw in IMAS 1.31.0.
Introduction to iGCUpdated 6 years ago

iGC Developers

Rendered from Introduction.Rmd in iGC 1.37.0.
iCNV VignetteUpdated 6 years ago

Zilu Zhou, Nancy R. Zhang

Rendered from iCNV-vignette.Rmd in iCNV 1.27.0.
iBMQ: An Integrated Hierarchical Bayesian Model for Multivariate eQTL MappingUpdated 6 years ago

Greg Imholte

Rendered from iBMQ.Rnw in iBMQ 1.47.0.
GOpro: Determine groups of genes and find their most characteristic GO termUpdated 6 years ago

Lidia Chrabaszcz

Rendered from GOpro_vignette.Rmd in GOpro 1.33.0.
gmapRUpdated 6 years ago

Michael Lawrence

Rendered from gmapR.Rnw in gmapR 1.49.0.
genomation: a toolkit for annotation and visualization of genomic dataUpdated 6 years ago

Altuna Akalin

Rendered from GenomationManual.Rmd in genomation 1.39.0.
geNetClassifier-vignetteUpdated 6 years ago

Sara Aibar

Rendered from geNetClassifier-vignette.Rnw in geNetClassifier 1.47.0.
FRGEpistasis: A Tool for Epistasis Analysis Based on Functional Regression ModelUpdated 6 years ago

Futao Zhang

Rendered from FRGEpistasis.Rnw in FRGEpistasis 1.43.0.
flowMatch: Cell population matching and meta-clustering in Flow CytometryUpdated 6 years ago

Ariful Azad

Rendered from flowMatch.Rnw in flowMatch 1.43.0.
How to Use Fit-Hi-C R PackageUpdated 6 years ago

Ruyu Tan

Rendered from fithic.Rmd in FitHiC 1.33.0.
fCIUpdated 6 years ago

Shaojun Tang

Rendered from fCI.Rmd in fCI 1.37.0.
Using DeMANDUpdated 6 years ago

Jung Hoon Woo

Rendered from DeMAND.Rnw in DeMAND 1.37.0.
deltaGsegUpdated 6 years ago

Diana Low

Rendered from deltaGseg.Rnw in deltaGseg 1.47.0.
How to apply the ddCt methodUpdated 6 years ago

Jitao David Zhang

Rendered from RT-PCR-Script-ddCt.Rnw in ddCt 1.63.0.
Using CODEXUpdated 6 years ago

Yuchao Jiang

Rendered from CODEX_vignettes.Rnw in CODEX 1.39.0.
CNVPanelizerUpdated 6 years ago

Thomas Wolf

Rendered from CNVPanelizer.Rnw in CNVPanelizer 1.39.0.
Main vignette:Playing with networks using CNORfuzzylUpdated 6 years ago

T. Cokelaer

Rendered from CNORfuzzy-vignette.Rnw in CNORfuzzy 1.49.0.
Using multiple time points to train logic models to dataUpdated 6 years ago

A. MacNamara

Rendered from CNORdt-vignette.Rnw in CNORdt 1.49.0.
Advanced baySeq analysesUpdated 6 years ago

Samuel Granjeaud

Rendered from clusterSeq.Rnw in clusterSeq 1.31.0.
Converting Rmarkdown to F1000Research LaTeX FormatUpdated 6 years ago

Mike L. Smith

Rendered from Generate_F1000_Latex.Rmd in BiocWorkflowTools 1.33.0.
Using BBCAnalyzerUpdated 6 years ago

Sarah Sandmann

Rendered from BBCAnalyzer.Rnw in BBCAnalyzer 1.37.0.
BaseSpaceRUpdated 6 years ago

Jared O'Connell

Rendered from BaseSpaceR.Rnw in BaseSpaceR 1.51.0.
Flexible isoform-level differential expression analysis with BallgownUpdated 6 years ago

Jack Fu

Rendered from ballgown.Rmd in ballgown 2.39.0.
REBET VignetteUpdated 6 years ago

Bill Wheeler

Rendered from vignette.Rnw in REBET 1.25.0.
SpacePAC: Identifying mutational clusters in 3D protein space using simulationUpdated 6 years ago

Gregory Ryslik

Rendered from SpacePAC.Rnw in SpacePAC 1.45.0.
iPAC: identification of Protein Amino acid MutationsUpdated 6 years ago

Gregory Ryslik

Rendered from GraphPAC.Rnw in GraphPAC 1.49.0.
SIMD TutorialUpdated 6 years ago

Yan Zhou

Rendered from SIMD.Rmd in SIMD 1.25.0.
twoddpcr: A package for Droplet Digital PCR analysisUpdated 6 years ago

Anthony Chiu

Rendered from twoddpcr.Rmd in twoddpcr 1.31.0.
Network Biology (Induced Subnetwork) VignetteUpdated 6 years ago

Michael T. Zimmermann

Rendered from subnetworks.Rmd in RITAN 1.31.0.
BRAIN UsageUpdated 6 years ago

Piotr Dittwald

Rendered from BRAIN-vignette.Rnw in BRAIN 1.53.0.
TPP_introduction_1DUpdated 6 years ago

Dorothee Childs

Rendered from TPP_introduction_1D.Rnw in TPP 3.35.0.
Choosing ResourcesUpdated 6 years ago

Michael T. Zimmermann

Rendered from choosing_resources.Rmd in RITAN 1.31.0.
SIMAT UsageUpdated 6 years ago

M. R. Nezami Ranjbar

Rendered from SIMAT-vignette.Rnw in SIMAT 1.39.0.
tRanslatomeUpdated 6 years ago

Toma Tebaldi

Rendered from tRanslatome_package.Rnw in tRanslatome 1.45.0.
CellTrails: Reconstruction, visualization, and analysis of branching trajectories from single-cell expression dataUpdated 6 years ago

Daniel Christian Ellwanger Stanford University School of Medicine Stanford, California, USA [email protected]

Rendered from vignette.Rmd in CellTrails 1.25.0.
Fitting and visualising row-linear models with \texttt{consensus}Updated 6 years ago

Tim Peters

Rendered from consensus.Rnw in consensus 1.25.0.
BUScorrect_user_guideUpdated 6 years ago

Xiangyu Luo

Rendered from BUScorrect_user_guide.Rnw in BUScorrect 1.25.0.
UsersGuideUpdated 6 years ago

Kevin Rue-Albrecht

Rendered from GOexpress-UsersGuide.Rnw in GOexpress 1.41.0.
Introduction to TVTBUpdated 6 years ago

Kévin Rue-Albrecht

Rendered from Introduction.Rmd in TVTB 1.33.0.
IntroductionUpdated 6 years ago

Diogo Veiga

Rendered from Introduction.Rmd in maser 1.25.0.
Mapping protein features to splicing eventsUpdated 6 years ago

Diogo Veiga

Rendered from Protein_mapping.Rmd in maser 1.25.0.
An introduction to RbowtieUpdated 6 years ago

Michael Stadler, Dimos Gaidatzis, Anita Lerch

Rendered from Rbowtie-Overview.Rmd in Rbowtie 1.47.0.
An introduction to Biobase and ExpressionSetsUpdated 6 years ago

Bioconductor Package Maintainer

Rendered from ExpressionSetIntroduction.Rnw in Biobase 2.67.0.
An Introduction to the GenomicAlignments PackageUpdated 6 years ago

Hervé Pagès

Rendered from GenomicAlignmentsIntroduction.Rnw in GenomicAlignments 1.43.0.
An Overview of the IRanges packageUpdated 6 years ago

Hervé Pagès

Rendered from IRangesOverview.Rnw in IRanges 2.41.1.
Introduction to MetIDUpdated 6 years ago

Xuchen Wang

Rendered from Introduction_to_MetID.Rmd in MetID 1.25.0.
Combining HDMSe/MSe data using synapter to optimise identification and quantitationUpdated 6 years ago

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered from synapter.Rmd in synapter 2.31.0.
DMRcallerUpdated 6 years ago

Nicolae Radu Zabet

Rendered from DMRcaller.Rnw in DMRcaller 1.39.0.
NormqPCR: Functions for normalisation of RT-qPCR dataUpdated 6 years ago

James Perkins

Rendered from NormqPCR.Rnw in NormqPCR 1.53.0.
Functions to load RT-qPCR data into RUpdated 6 years ago

James Perkins

Rendered from ReadqPCR.Rnw in ReadqPCR 1.53.0.
ipdDbUpdated 6 years ago

Steffen Klasberg

Rendered from Readme.Rmd in ipdDb 1.25.0.
Total affinity and occupanciesUpdated 6 years ago

Elena Grassi

Rendered from MatrixRider.Rnw in MatrixRider 1.39.0.
omicplotR: A tool for visualizing omic datasets as compositionsUpdated 6 years ago

Daniel Giguere, Jean Macklaim, Greg Gloor

Rendered from omicplotR.Rmd in omicplotR 1.27.0.
Using mygene.RUpdated 6 years ago

Adam Mark, Cyrus Afrasiabi, Chunlei Wu

Rendered from mygene.Rnw in mygene 1.43.0.
Facilities for Filtering Bioconductor Annotation ResourcesUpdated 6 years ago

Bioconductor Package Maintainer

Rendered from AnnotationFilter.Rmd in AnnotationFilter 1.31.0.
Methylation status calling with METHimputeUpdated 6 years ago

Aaron Taudt

Rendered from methimpute.Rnw in methimpute 1.29.0.
Introduction to MetaCytoUpdated 6 years ago

Zicheng Hu

Rendered from MetaCyto_Vignette.Rmd in MetaCyto 1.29.0.
GIGSEA: Genotype Imputed Gene Set Enrichment AnalysisUpdated 6 years ago

| Shijia Zhu | Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

Rendered from GIGSEA_tutorial.Rmd in GIGSEA 1.25.0.
Pathway Analysis of Metabolic ActivitiesUpdated 7 years ago

Gabriele Sales

Rendered from metabolites.pdf.asis in graphite 1.53.0.
Analysing transcript 5'-profiling data using iceteaUpdated 7 years ago

Vivek Bhardwaj and Thomas Manke

Rendered from mapcap_analysis.Rmd in icetea 1.25.0.
A Guide to using BiFETUpdated 7 years ago

Ahrim Youn

Rendered from BiFET.Rmd in BiFET 1.27.0.
Causal Effect Analysis of Risk Factors for Disease with the "GMRP" packageUpdated 7 years ago

Yuan-De Tan

Rendered from GMRP.Rnw in GMRP 1.35.0.
Steady-state analysis of flow cytometry dataUpdated 7 years ago

R Clay Wright

Rendered from steady-state-vignette.Rmd in flowTime 1.31.0.
Detecting hidden heterogeneity in single cell RNA-Seq dataUpdated 7 years ago

Donghyung Lee

Rendered from detecting_hidden_heterogeneity_iasvaV0.95.Rmd in iasva 1.25.0.
Analysing RNA-Seq count data with the "MBttest" packageUpdated 7 years ago

Yuan-De Tan

Rendered from MBttest.Rnw in MBttest 1.35.0.
STATegRa User's GuideUpdated 7 years ago

The STATegra Consortium

Rendered from STATegRa.Rmd in STATegRa 1.43.0.
Working with Illumina basecalling and demultiplexing data using the basecallQC packageUpdated 7 years ago

Thomas Carroll, Marian Dore

Rendered from basecallQC.Rmd in basecallQC 1.31.0.
goProfiles VignetteUpdated 7 years ago

Alex Sanchez

Rendered from goProfiles.Rnw in goProfiles 1.69.0.
ivygapSE -- Bioconductor container for Ivy-GAP expression and metadataUpdated 7 years ago

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered from ivygapSE.Rmd in ivygapSE 1.29.0.
Missing value handlingUpdated 7 years ago

Arne Smits

Rendered from MissingValues.Rmd in DEP 1.29.0.
Introduction to Using RSeqAnUpdated 7 years ago

August Guang

Rendered from first_example.Rmd in RSeqAn 1.27.0.
MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array dataUpdated 7 years ago

L.J.Sinke

Rendered from MethylAid.Rnw in MethylAid 1.41.0.
Make Genome-level Trellis GraphUpdated 7 years ago

Zuguang Gu

Rendered from gtrellis.Rmd in gtrellis 1.39.0.
scDD QuickstartUpdated 7 years ago

Keegan Korthauer

Rendered from scDD.Rnw in scDD 1.31.0.
Designing and analyzing multiplex PCR primers with openPrimeRUpdated 7 years ago

Matthias Döring

Rendered from openPrimeR_vignette.Rmd in openPrimeR 1.29.0.
HOWTO: Use the online query toolsUpdated 7 years ago

Bioconductor Package Maintainer

Rendered from query.Rnw in annotate 1.85.0.
Relationships Among ResourcesUpdated 7 years ago

Michael T. Zimmermann

Rendered from resource_relationships.Rmd in RITAN 1.31.0.
CpG setsUpdated 7 years ago

Andrey A Shabalin

Rendered from RW2_CpG_sets.Rmd in ramwas 1.31.0.
RaMWAS ParametersUpdated 7 years ago

Andrey A Shabalin

Rendered from RW6_param.Rmd in ramwas 1.31.0.
Manual for the TTMap libraryUpdated 7 years ago

Rachel Jeitziner

Rendered from TTMap.Rnw in TTMap 1.29.0.
Finding Ideal KUpdated 7 years ago

Tyler J Burns

Rendered from FindingIdealK.Rmd in Sconify 1.27.0.
Step 1: Pre-ProcessingUpdated 7 years ago

Tyler J Burns

Rendered from Step1.PreProcessing.Rmd in Sconify 1.27.0.
Assessing quality of CyTOF data with KNNUpdated 7 years ago

Tyler J Burns

Rendered from DataQuality.Rmd in Sconify 1.27.0.
Bioconductor LaTeX StyleUpdated 7 years ago

Benedikt G. Brink

Rendered from ddPCRclust.Rnw in ddPCRclust 1.27.0.
Step 2: The Scone WorkflowUpdated 7 years ago

Tyler J Burns

Rendered from Step2.TheSconeWorkflow.Rmd in Sconify 1.27.0.
Step 3: Post-ProcessingUpdated 7 years ago

Tyler J Burns

Rendered from Step3.PostProcessing.Rmd in Sconify 1.27.0.
Introduction to gep2pepUpdated 7 years ago

Francesco Napolitano

Rendered from vignette.Rmd in gep2pep 1.27.0.
Overlap encodingsUpdated 7 years ago

Hervé Pagès

Rendered from OverlapEncodings.Rnw in GenomicAlignments 1.43.0.
BeadDataPackR VignetteUpdated 7 years ago

Mike Smith

Rendered from BeadDataPackR.rnw in BeadDataPackR 1.59.0.
Choosing a LOLA UniverseUpdated 7 years ago

Nathan Sheffield

Rendered from choosingUniverse.Rmd in LOLA 1.37.0.
Using LOLA CoreUpdated 7 years ago

Nathan Sheffield

Rendered from usingLOLACore.Rmd in LOLA 1.37.0.
Creating annotated output with \Biocpkg{affycoretools} and ReportingToolsUpdated 7 years ago

James W. MacDonald

Rendered from RefactoredAffycoretools.Rmd in affycoretools 1.79.0.
Clustering time series gene expression data with TMixClustUpdated 7 years ago

Monica Golumbeanu

Rendered from TMixClust.Rnw in TMixClust 1.29.0.
NanoStringDiff VignetteUpdated 7 years ago

tingting zhai

Rendered from NanoStringDiff.Rnw in NanoStringDiff 1.37.0.
ChIPexoQual: A quality control pipeline for ChIP-exo/nexus data.Updated 7 years ago

| Rene Welch and Sündüz Keleş | Department of Statistics, University of Wisconsin-Madison

Rendered from vignette.Rmd in ChIPexoQual 1.31.0.
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLsUpdated 7 years ago

Tianlei Xu

Rendered from loci2path-vignette.Rmd in loci2path 1.27.0.
A package for importing and analyzing data from Roche's Genome Sequencer SystemUpdated 7 years ago

Hans-Ulrich Klein

Rendered from vignette.Rnw in R453Plus1Toolbox 1.57.0.
Synapter2 and synergise2Updated 7 years ago

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered from synapter2.Rmd in synapter 2.31.0.
Bioconductor LaTeX Style 2.0Updated 7 years ago

Bioconductor Package Maintainer

Rendered from LatexStyle2.Rnw in BiocStyle 2.35.0.
Organism.dplyrUpdated 7 years ago

Martin Morgan

Rendered from Organism.dplyr.Rmd in Organism.dplyr 1.35.0.
Joint Analysis of Methylation and Genotype DataUpdated 7 years ago

Andrey A Shabalin

Rendered from RW4_SNPs.Rmd in ramwas 1.31.0.
BAM Quality Control MeasuresUpdated 7 years ago

Andrey A Shabalin

Rendered from RW3_BAM_QCs.Rmd in ramwas 1.31.0.
omicsPrint: detection of data linkage errors in multiple omics studiesUpdated 7 years ago

Maarten van Iterson, Davy Cats, Paul Hop, Bas T. Heijmans

Rendered from omicsPrint.Rmd in omicsPrint 1.27.0.
GDCRNATools: integrative analysis of protein coding genes, long non-coding genes, and microRNAs in GDCUpdated 7 years ago

Ruidong Li and Han Qu

Rendered from index.Rmd in GDCRNATools 1.27.0.
Using cytolibUpdated 7 years ago

Mike Jiang

Rendered from cytolib.Rmd in cytolib 2.19.0.
using rCGH packageUpdated 7 years ago

Frederic Commo

Rendered from rCGH.Rnw in rCGH 1.37.0.
Identify differential APA usage from RNA-seq alignmentsUpdated 7 years ago

Elena Grassi

Rendered from roar.Rnw in roar 1.43.0.
Introduction to slalomUpdated 7 years ago

Davis McCarthy and Florian Buettner

Rendered from vignette.Rmd in slalom 1.29.0.
Applying MIRA to a Biological QuestionUpdated 7 years ago

John Lawson

Rendered from BiologicalApplication.Rmd in MIRA 1.29.0.
NCIgraph: networks from the NCI pathway integrated database as graphNEL objects.Updated 7 years ago

Laurent Jacob

Rendered from NCIgraph.Rnw in NCIgraph 1.55.0.
fastLiquidAssociation VignetteUpdated 7 years ago

Tina Gunderson

Rendered from fastLiquidAssociation.Rnw in fastLiquidAssociation 1.43.0.
Monocle: Cell counting, differential expression, and trajectory analysis for single-cell RNA-Seq experimentsUpdated 7 years ago

Cole Trapnell

Rendered from monocle-vignette.Rnw in monocle 2.35.0.
clipperUpdated 7 years ago

Paolo Martini

Rendered from clipper.Rnw in clipper 1.47.0.
The minfi User's GuideUpdated 7 years ago

Kasper D. Hansen, Jean-Phillipe Fortin

Rendered from minfi.Rmd in minfi 1.53.1.
chromVARUpdated 7 years ago

Alicia Schep

Rendered from Introduction.Rmd in chromVAR 1.29.0.
GA4GHclientUpdated 7 years ago

Welliton Souza

Rendered from GA4GHclient.Rmd in GA4GHclient 1.31.0.
GA4GHshinyUpdated 7 years ago

Welliton Souza

Rendered from GA4GHshiny.Rmd in GA4GHshiny 1.29.0.
Oncomix VignetteUpdated 7 years ago

Daniel G. Piqué

Rendered from oncomix.Rmd in oncomix 1.29.0.
Introduction to the motifcounter packageUpdated 7 years ago

Wolfgang Kopp

Rendered from motifcounter.Rmd in motifcounter 1.31.0.
blima an R package for Bead Level Illumina Microarray AnalysisUpdated 7 years ago

Vojtěch Kulvait

Rendered from blima.rnw in blima 1.41.0.
MetaboSignalUpdated 7 years ago

Andrea Rodriguez-Martinez

Rendered from MetaboSignal.Rmd in MetaboSignal 1.37.0.
Using hiReadsProcessorUpdated 7 years ago

Nirav V Malani

Rendered from Tutorial.Rmd in hiReadsProcessor 1.43.0.
An overview of FELLA: data enrichment for metabolomics summary dataUpdated 7 years ago

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered from quickstart.Rmd in FELLA 1.27.0.
Annotated and regular heatmapsUpdated 7 years ago

Alexander Ploner

Rendered from annHeatmap.Rnw in Heatplus 3.15.0.
Rain UsageUpdated 7 years ago

Paul F. Thaben

Rendered from rain.Rnw in rain 1.41.0.
ABSSeqUpdated 7 years ago

Wentao Yang

Rendered from ABSSeq.Rnw in ABSSeq 1.61.0.
Introduction to SeqVarToolsUpdated 7 years ago

Stephanie M. Gogarten

Rendered from SeqVarTools.Rnw in SeqVarTools 1.45.0.
Cheatsheet for MultiAssayExperimentUpdated 7 years ago

Marcel Ramos

Rendered from MultiAssayExperiment_cheatsheet.pdf.asis in MultiAssayExperiment 1.33.1.
CummeRbund User GuideUpdated 7 years ago

Loyal A. Goff

Rendered from cummeRbund-manual.Rnw in cummeRbund 2.49.0.
Introduction to zFPKM TransformationUpdated 7 years ago

Ron Ammar

Rendered from zFPKM.Rmd in zFPKM 1.29.0.
Basic4Cseq: an R/Bioconductor package for the analysis of 4C-seq dataUpdated 7 years ago

Carolin Walter

Rendered from vignette.Rnw in Basic4Cseq 1.43.0.
Diffusion using diffuStats in a nutshellUpdated 7 years ago

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered from intro.Rmd in diffuStats 1.27.0.
SpacePAC: Identifying mutational clusters in 3D protein space using simulationUpdated 7 years ago

Gregory Ryslik

Rendered from QuartPAC.Rnw in QuartPAC 1.39.0.
Using Branchpointer for annotation of intronic human splicing branchpointsUpdated 7 years ago

Beth Signal

Rendered from branchpointer.Rnw in branchpointer 1.33.0.
Basics of the DiffLogo packageUpdated 7 years ago

Hendrik Treutler

Rendered from DiffLogoBasics.Rnw in DiffLogo 2.31.0.
Gene set and data preparationUpdated 7 years ago

Weijun Luo

Rendered from dataPrep.Rnw in gage 2.57.0.
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq dataUpdated 7 years ago

Carolin Walter

Rendered from vignette.Rnw in Scale4C 1.29.0.
KEGGlincs WorkflowsUpdated 7 years ago

Shana White

Rendered from Example-workflow.Rmd in KEGGlincs 1.33.0.
The gcapc user's guideUpdated 7 years ago

| Mingxiang Teng [email protected] | Rafael A. Irizarry [email protected] | Department of Biostatistics, Dana-Farber Cancer Institute & | Harvard T.H. Chan School of Public Health, Boston, MA, USA

Rendered from gcapc.Rmd in gcapc 1.31.0.
SAFE manualUpdated 7 years ago

Ludwig Geistlinger

Rendered from SAFEmanual3.Rnw in safe 3.47.0.
motifmatchrUpdated 8 years ago

Alicia Schep

Rendered from motifmatchr.Rmd in motifmatchr 1.29.0.
AllelicImbalance VignetteUpdated 8 years ago

Jesper R. Gadin and Lasse Folkersen

Rendered from AllelicImbalance-vignette.Rmd in AllelicImbalance 1.45.0.
msgbsR_ExampleUpdated 8 years ago

Benjamin Mayne

Rendered from msgbsR_Vignette.Rnw in msgbsR 1.31.0.
\maketitleMAIT VignetteUpdated 8 years ago

Pol Sola-Santos

Rendered from MAIT_Vignette.Rnw in MAIT 1.41.0.
heatmaps vignetteUpdated 8 years ago

Malcolm Perry

Rendered from heatmaps.Rmd in heatmaps 1.31.0.
The conumee vignetteUpdated 8 years ago

Volker Hovestadt, Marc Zapatka (Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany)

Rendered from conumee.Rmd in conumee 1.41.0.
epigenomix package vignetteUpdated 8 years ago

Hans-Ulrich Klein

Rendered from epigenomix.Rnw in epigenomix 1.47.0.
Similarity between two ChIP-Seq profilesUpdated 8 years ago

Astrid Deschênes

Rendered from similaRpeak.Rmd in similaRpeak 1.39.0.
Time course analysis of flow cytometry dataUpdated 8 years ago

R Clay Wright

Rendered from time-course-vignette.Rmd in flowTime 1.31.0.
SomaticSignaturesUpdated 8 years ago

Julian Gehring

Rendered from SomaticSignatures-vignette.Rhtml in SomaticSignatures 2.43.0.
IVAS : Identification of genetic Variants affecting Alternative SplicingUpdated 8 years ago

Seonggyun Han

Rendered from IVAS.Rnw in IVAS 2.27.0.
RareVariantVisUpdated 8 years ago

Tomasz Stokowy

Rendered from RareVariantsVis.Rnw in RareVariantVis 2.35.0.
geneClassifiers and missing probesetsUpdated 8 years ago

R Kuiper

Rendered from MissingCovariates.Rnw in geneClassifiers 1.31.0.
geneClassifiers introductionUpdated 8 years ago

R Kuiper

Rendered from geneClassifiers.Rnw in geneClassifiers 1.31.0.
Nucleosome PositioningUpdated 8 years ago

Astrid Deschênes

Rendered from RJMCMCNucleosomes.Rmd in RJMCMCNucleosomes 1.31.0.
Extending GenomicRanges Updated 8 years ago

Hervé Pagès

Rendered from ExtendingGenomicRanges.Rnw in GenomicRanges 1.59.1.
Reporting on microarray differential expressionUpdated 8 years ago

Jason A. Hackney

Rendered from microarrayAnalysis.Rnw in ReportingTools 2.47.0.
An Introduction to the BUMHMM pipelineUpdated 8 years ago

Alina Selega

Rendered from BUMHMM.Rnw in BUMHMM 1.31.0.
CausalR : an R Package for causal reasoning on networksUpdated 8 years ago

Glyn Bradley

Rendered from CausalR.rnw in CausalR 1.39.0.
riboSeqRUpdated 8 years ago

Samuel Granjeaud

Rendered from riboSeqR.Rnw in riboSeqR 1.41.0.
Shearwater MLUpdated 8 years ago

Inigo Martincorena and Moritz Gerstung

Rendered from shearwaterML.Rmd in deepSNV 1.53.0.
An introduction to CCPROMISEUpdated 8 years ago

Xueyuan Cao

Rendered from CCPROMISE.Rnw in CCPROMISE 1.33.0.
flowCleanUpdated 8 years ago

Kipper Fletez-Brant

Rendered from flowClean.Rnw in flowClean 1.45.0.
Pairwise whole genome alignmentUpdated 8 years ago

Ge Tan

Rendered from PairwiseWholeGenomeAlignment.Rmd in CNEr 1.43.0.
uSORT: Quick StartUpdated 8 years ago

Hao Chen

Rendered from uSORT_quick_start.Rmd in uSORT 1.33.0.
RankProd TutorialUpdated 8 years ago

Francesco Del Carratore

Rendered from RankProd.Rnw in RankProd 3.33.0.
Introduction to HiTC packageUpdated 8 years ago

Nicolas Servant

Rendered from HiTC.Rnw in HiTC 1.51.0.
CNE identification and visualisationUpdated 8 years ago

Ge Tan

Rendered from CNEr.Rmd in CNEr 1.43.0.
MOSAiCSUpdated 8 years ago

Dongjun Chung

Rendered from mosaics-example.Rnw in mosaics 2.45.0.
Visualize GatingSet with ggcytoUpdated 8 years ago

Mike Jiang

Rendered from ggcyto.GatingSet.Rmd in ggcyto 1.35.0.
GeneGeneInteR IntroductionUpdated 8 years ago

Mathieu Emily

Rendered from VignetteGeneGeneInteR_Introduction.Rnw in GeneGeneInteR 1.33.0.
ASAFE (Ancestry Specific Allele Frequency Estimation)Updated 8 years ago

Qian Zhang

Rendered from ASAFE.Rmd in ASAFE 1.33.0.
mirIntegrator OverviewUpdated 8 years ago

Diana Diaz

Rendered from mirIntegrator.Rnw in mirIntegrator 1.37.0.
GSALightning: Ultra-fast Permutation-based Gene Set AnalysisUpdated 8 years ago

Billy Heung Wing Chang

Rendered from vignette.Rmd in GSALightning 1.35.0.
eudysbiome User ManualUpdated 8 years ago

Xiaoyuan Zhou

Rendered from eudysbiome.Rnw in eudysbiome 1.37.0.
GenomicTuples: Classes and MethodsUpdated 9 years ago

Peter Hickey

Rendered from GenomicTuplesIntroduction.Rmd in GenomicTuples 1.41.1.
netprioR VignetteUpdated 9 years ago

Fabian Schmich

Rendered from netprioR.Rmd in netprioR 1.33.0.
Tutorial on How to Use the Functions in the \texttt{attract} PackageUpdated 9 years ago

Samuel Zimmerman

Rendered from attract.Rnw in attract 1.59.0.
CHiCAGO VignetteUpdated 9 years ago

Jonathan Cairns, Paula Freire-Pritchett, Mikhail Spivakov

Rendered from Chicago.Rmd in Chicago 1.35.0.
An Introduction to the pandaR PackageUpdated 9 years ago

Daniel Schlauch, Albert Young, Joseph N. Paulson

Rendered from pandaR.Rmd in pandaR 1.39.0.
An Introduction to the MMDiff2 methodUpdated 9 years ago

Gabriele Schweikert

Rendered from MMDiff2.Rnw in MMDiff2 1.35.0.
Using mzIDUpdated 9 years ago

Laurent Gatto

Rendered from HOWTO_mzID.Rnw in mzID 1.45.0.
LedPred ExampleUpdated 9 years ago

Aitor Gonzalez

Rendered from LedPred.Rnw in LedPred 1.41.0.
The biomformat package vignetteUpdated 9 years ago

Paul J. McMurdie

Rendered from biomformat.Rmd in biomformat 1.35.0.
ROntoToolsUpdated 9 years ago

Sorin Draghici

Rendered from rontotools.Rnw in ROntoTools 2.35.0.
Introduction to the bamsignals packageUpdated 9 years ago

Alessandro Mammana and Johannes Helmuth

Rendered from bamsignals.Rmd in bamsignals 1.39.0.
CONFESSUpdated 9 years ago

Diana LOW

Rendered from vignette_tex.Rnw in CONFESS 1.35.0.
Subclonal variant calling with multiple samples and prior knowledge using shearwaterUpdated 9 years ago

Moritz Gerstung

Rendered from shearwater.Rnw in deepSNV 1.53.0.
Normalization of 450K dataUpdated 9 years ago

Jonathan Alexander Heiss

Rendered from read_and_normalize450K.Rnw in normalize450K 1.35.0.
odseq package vignetteUpdated 9 years ago

Mantainer: [email protected]

Rendered from vignette.Rmd in odseq 1.35.0.
Assessing gene relevance for a set of phenotypesUpdated 9 years ago

Patrice Godard and Matt Page

Rendered from PCAN.Rmd in PCAN 1.35.0.
doppelgangRUpdated 9 years ago

Levi Waldron

Rendered from doppelgangR.Rmd in doppelgangR 1.35.0.
Introduction and Methodological DetailsUpdated 9 years ago

Christian Arnold, Pooja Bhat, Judith Zaugg

Rendered from IntroductionToSNPhood.Rmd in SNPhood 1.37.0.
OmicCircos vignetteUpdated 9 years ago

Ying Hu

Rendered from OmicCircos_vignette.Rnw in OmicCircos 1.45.0.
Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and exampleUpdated 9 years ago

Jitao David Zhang

Rendered from rtPCR.Rnw in ddCt 1.63.0.
Power and Sample size analysis for gene expression from RNA-seqUpdated 9 years ago

Hao Wu

Rendered from PROPER.Rnw in PROPER 1.39.0.
biomvRCNS package introductionUpdated 9 years ago

Yang Du

Rendered from biomvRCNS.Rnw in biomvRCNS 1.47.0.
An Introduction to BiSeqUpdated 9 years ago

Katja Hebestreit

Rendered from BiSeq.Rnw in BiSeq 1.47.0.
Introduction to cycleUpdated 9 years ago

Matthias Futschik

Rendered from cycle.Rnw in cycle 1.61.0.
Introduction to OLINguiUpdated 9 years ago

Matthias Futschik

Rendered from OLINgui.Rnw in OLINgui 1.81.0.
A R/Bioconductor package for basic peak calling on STARR-seq dataUpdated 9 years ago

Annika Buerger

Rendered from BasicSTARRseq.rnw in BasicSTARRseq 1.35.0.
RGraph2jsUpdated 9 years ago

Stephane Cano

Rendered from RGraph2js.Rnw in RGraph2js 1.35.0.
Path2PPI - Tutorial, example and the algorithmUpdated 9 years ago

Oliver Philipp and Ina Koch ([email protected])

Rendered from Path2PPI-tutorial.Rmd in Path2PPI 1.37.0.
RUVnormalizeUpdated 9 years ago

Laurent Jacob

Rendered from RUVnormalize.Rnw in RUVnormalize 1.41.0.
Empirical Browns MethodUpdated 9 years ago

David L Gibbs

Rendered from ebmVignette.Rmd in EmpiricalBrownsMethod 1.35.0.
seqTools_qual_reportUpdated 9 years ago

Wolfgang Kaisers

Rendered from seqTools_qual_report.Rnw in seqTools 1.41.0.
EBcoexpress DemoUpdated 9 years ago

John A. Dawson

Rendered from EBcoexpressVignette.Rnw in EBcoexpress 1.51.0.
Genome metadataUpdated 9 years ago

Chris Stubben

Rendered from genomes.Rnw in genomes 3.37.0.
chromDrawUpdated 9 years ago

Jan Janecka

Rendered from chromDraw.Rnw in chromDraw 2.37.0.
Using profileScoreDistUpdated 9 years ago

| Pål O. Westermark | Carité University Medicine Berlin

Rendered from profileScoreDist-vignette.Rmd in profileScoreDist 1.35.0.
GSCAUpdated 9 years ago

Zhicheng Ji

Rendered from GSCA.Rnw in GSCA 2.37.0.
Perform GWAS trait-associated SNP enrichment analyses in genomic intervalsUpdated 9 years ago

li chen

Rendered from traseR.Rnw in traseR 1.37.0.
R4RNAUpdated 9 years ago

Daniel Lai

Rendered from R4RNA.Rnw in R4RNA 1.35.0.
CGEN VignetteUpdated 9 years ago

Justin Lee

Rendered from vignette.Rnw in CGEN 3.43.0.
Assessment and comparison of miRNA expression estimation methods (miRcomp)Updated 9 years ago

Matthew N. McCall

Rendered from miRcomp.Rmd in miRcomp 1.37.0.
Using the SICtools PackageUpdated 9 years ago

Xiaobin Xing

Rendered from SICtools.Rmd in SICtools 1.37.0.
Overview of the 'PWMEnrich' packageUpdated 9 years ago

Diego Diez

Rendered from PWMEnrich.Rnw in PWMEnrich 4.43.0.
DNABarcodesUpdated 9 years ago

Tilo Buschmann

Rendered from DNABarcodes.Rmd in DNABarcodes 1.37.0.
Data inputUpdated 9 years ago

David Clayton

Rendered from data-input-vignette.Rnw in snpStats 1.57.0.
Using MyVariant.RUpdated 9 years ago

Adam Mark, Chunlei Wu

Rendered from myvariant.Rnw in myvariant 1.37.0.
Oscope_vigetteUpdated 9 years ago

Ning Leng

Rendered from Oscope_vignette.Rnw in Oscope 1.37.0.
EMDomics VignetteUpdated 9 years ago

Sadhika Malladi and Daniel Schmolze

Rendered from EMDomics.Rmd in EMDomics 2.37.0.
diffHic VignetteUpdated 9 years ago

Aaron Lun

Rendered from diffHic.Rnw in diffHic 1.39.0.
Manual for the casper libraryUpdated 9 years ago

David Rossell

Rendered from casper.Rnw in casper 2.41.0.
PECA: Probe-level Expression Change AveragingUpdated 9 years ago

Tomi Suomi

Rendered from PECA.Rnw in PECA 1.43.0.
User manual for R-Package hierGWASUpdated 9 years ago

Laura Buzdugan

Rendered from hierGWAS.Rnw in hierGWAS 1.37.0.
compEpiToolsUpdated 9 years ago

Mattia Furlan

Rendered from compEpiTools.rnw in compEpiTools 1.41.0.
TSCAN: Tools for Single-Cell ANalysisUpdated 9 years ago

Zhicheng Ji

Rendered from TSCAN.Rnw in TSCAN 1.45.0.
Identification of Differentially Expressed Genes with Artificial ComponentsUpdated 10 years ago

Juan Pablo Acosta

Rendered from acde.Rnw in acde 1.37.0.
DART TutorialUpdated 10 years ago

Charles Shijie Zheng

Rendered from DART.Rnw in DART 1.55.0.
MBASEDUpdated 10 years ago

Oleg Mayba

Rendered from MBASED.Rnw in MBASED 1.41.0.
Working with Illumina 450k Arrays using methylumiUpdated 10 years ago

Sean Davis

Rendered from methylumi450k.Rnw in methylumi 2.53.0.
soggiUpdated 10 years ago

Tom Carroll

Rendered from soggi.Rnw in soGGi 1.39.0.
methylPipeUpdated 10 years ago

Mattia Furlan

Rendered from methylPipe.rnw in methylPipe 1.41.0.
seqPatternUpdated 10 years ago

Vanja Haberle

Rendered from seqPattern.Rnw in seqPattern 1.39.0.
GOTHiCUpdated 10 years ago

Borbala Mifsud

Rendered from package_vignettes.Snw in GOTHiC 1.43.0.
Running gene set enrichment analysis with the "npGSEA" packageUpdated 10 years ago

Jessica Larson

Rendered from npGSEA.Rnw in npGSEA 1.43.0.
RSVSim: an R/Bioconductor package for the simulation of structural variationsUpdated 10 years ago

Christoph Bartenhagen

Rendered from vignette.Rnw in RSVSim 1.47.0.
cnvGSA - Gene-Set Analysis of Rare Copy Number VariantsUpdated 10 years ago

Joseph Lugo

Rendered from cnvGSA-vignette.Rnw in cnvGSA 1.51.0.
Running gene set analyses with the "cpvSNP" packageUpdated 10 years ago

Caitlin McHugh

Rendered from cpvSNP.Rnw in cpvSNP 1.39.0.
Qualitative Biclustering with Bioconductor Package rqubicUpdated 10 years ago

Jitao David Zhang

Rendered from rqubic.Rnw in rqubic 1.53.0.
LBE VignetteUpdated 10 years ago

Cyril Dalmasso

Rendered from LBE.Rnw in LBE 1.75.0.
Introduction to MethTargetedNGSUpdated 10 years ago

Muhammad Ahmer Jamil

Rendered from MethTargetedNGS.Rnw in MethTargetedNGS 1.39.0.
qvalue PackageUpdated 10 years ago

John D. Storey

Rendered from qvalue.Rnw in qvalue 2.39.0.
FISHAlyseR Automated fluorescence in situ hybridisation quantification in RUpdated 10 years ago

Karesh Arunakirinathan

Rendered from FISHalyseR.Rnw in FISHalyseR 1.41.0.
User manual for R-Package PMMUpdated 10 years ago

Anna Drewek

Rendered from pmm-package.Rnw in pmm 1.39.0.
lpNet, network inference with a linear optimization program.Updated 10 years ago

Lars Kaderali

Rendered from vignette_lpNet.Rnw in lpNet 2.39.0.
Introduction to the TIN packageUpdated 10 years ago

Bjarne Johannessen

Rendered from TIN.Rnw in TIN 1.39.0.
Introduction to ChIPseqRUpdated 10 years ago

Peter Humburg

Rendered from Introduction.Rnw in ChIPseqR 1.61.0.
A guide to using muscleUpdated 10 years ago

Alex T. Kalinka

Rendered from muscle-vignette.Rnw in muscle 3.49.0.
SigSquaredUpdated 10 years ago

UnJin Lee

Rendered from sigsquared.Rnw in sigsquared 1.39.0.
Motif Discovery with SELEX-seqUpdated 10 years ago

Harmen J. Bussemaker

Rendered from SELEX.Rnw in SELEX 1.39.0.
r3CseqUpdated 10 years ago

Supat Thongjuea

Rendered from r3Cseq.Rnw in r3Cseq 1.53.0.
An R Package for processing expression microarray dataUpdated 10 years ago

Benny Chain

Rendered from agilp_manual.Rnw in agilp 3.39.0.
Introduction to proBAMrUpdated 10 years ago

Xiaojing Wang

Rendered from proBAMr.Rnw in proBAMr 1.41.0.
Estimate eQTL networks using qpgraphUpdated 10 years ago

Robert Castelo

Rendered from eQTLnetworks.Rnw in qpgraph 2.41.0.
Simulating molecular regulatory networks using qpgraphUpdated 10 years ago

Robert Castelo

Rendered from qpgraphSimulate.Rnw in qpgraph 2.41.0.
Streamer: A simple exampleUpdated 10 years ago

Martin Morgan

Rendered from Streamer.Rnw in Streamer 1.53.0.
Analyze flow cytometric data using gate informationUpdated 10 years ago

Joachim Schumann

Rendered from flowCyBar-manual.Rnw in flowCyBar 1.43.0.
Analyze flow cytometric data using histogram informationUpdated 10 years ago

Author: Joachim Schumann

Rendered from flowCHICmanual.Rnw in flowCHIC 1.41.0.
Usecases for isobar packageUpdated 10 years ago

Florian P Breitwieser

Rendered from isobar-usecases.Rnw in isobar 1.53.0.
A Markdown Vignette with knitrUpdated 10 years ago

Hoang Tan Nguyen

Rendered from CNVrd2.Rnw in CNVrd2 1.45.0.
ccrepeUpdated 10 years ago

Emma Schwager

Rendered from ccrepe.Rnw in ccrepe 1.43.0.
Introduction to pepXMLTabUpdated 10 years ago

Xiaojing Wang

Rendered from pepXMLTab.Rnw in pepXMLTab 1.41.0.
IntroductionUpdated 10 years ago

Wolfgang Kaisers

Rendered from seqTools.Rnw in seqTools 1.41.0.
Creating IGV HTML reports with tracktablesUpdated 10 years ago

Tom Carroll

Rendered from tracktables.Rnw in tracktables 1.41.0.
An R Package for Predicting Binary Labels in Partially-Labeled GraphsUpdated 10 years ago

Marco Frasca

Rendered from COSNet_v.Rnw in COSNet 1.41.0.
MBAmethyl VignetteUpdated 10 years ago

Tao Wang

Rendered from MBAmethyl.Rnw in MBAmethyl 1.41.0.
IMPCdata VignetteUpdated 10 years ago

Jeremy Mason

Rendered from IMPCdata.Rnw in IMPCdata 1.43.0.
Association Studies using Generalized Structured Equation Models.Updated 10 years ago

Hela Romdhani

Rendered from ASGSCA.Rnw in ASGSCA 1.41.0.
Using MGFMUpdated 10 years ago

Khadija El Amrani

Rendered from MGFM.Rnw in MGFM 1.41.0.
SigFuge TutorialUpdated 10 years ago

Patrick Kimes

Rendered from SigFuge.Rnw in SigFuge 1.45.0.
massiR_ExampleUpdated 10 years ago

Sam Buckberry

Rendered from massiR_Vignette.Rnw in massiR 1.43.0.
AIMS An Introduction (HowTo)Updated 10 years ago

Eric R Paquet

Rendered from AIMS.Rnw in AIMS 1.39.0.
Principal components analysisUpdated 10 years ago

David Clayton

Rendered from pca-vignette.Rnw in snpStats 1.57.0.
runLCUpdated 10 years ago

Yann Guitton

Rendered from runLC.Rnw in metaMS 1.43.0.
cisPathUpdated 10 years ago

Likun Wang

Rendered from cisPath.Rnw in cisPath 1.47.0.
MultiMedTutorialUpdated 10 years ago

Simina M. Boca

Rendered from MultiMed.Rnw in MultiMed 2.29.0.
UNDO UsageUpdated 10 years ago

Niya Wang

Rendered from UNDO-vignette.Rnw in UNDO 1.49.0.
An introduction to PROMISEUpdated 10 years ago

Stan Pounds

Rendered from PROMISE.Rnw in PROMISE 1.59.0.
The Pviz users guideUpdated 10 years ago

Renan Sauteraud

Rendered from Pviz.Rnw in Pviz 1.41.0.
Full peptide microarray analysisUpdated 10 years ago

Gregory C Imholte

Rendered from pepStat.Rnw in pepStat 1.41.0.
RRHOUpdated 10 years ago

Jonathan Rosenblatt

Rendered from RRHO.Rnw in RRHO 1.47.0.
flowBinUpdated 10 years ago

Kieran O'Neill

Rendered from flowBin.Rnw in flowBin 1.43.0.
cosmiq primerUpdated 10 years ago

David Fischer

Rendered from cosmiq.Rnw in cosmiq 1.41.0.
flowMeans: Non-parametric Flow Cytometry Data GatingUpdated 10 years ago

Nima Aghaeepour

Rendered from flowMeans.Rnw in flowMeans 1.67.0.
Introduction to RGSEAUpdated 10 years ago

Chengcheng Ma

Rendered from RGSEA.Rnw in RGSEA 1.41.0.
cn.farms: Manual for the R packageUpdated 11 years ago

Andreas Mitterecker

Rendered from cn.farms.Rnw in cn.farms 1.55.0.
An Introduction to biovizBaseUpdated 11 years ago

Michael Lawrence

Rendered from intro.Rnw in biovizBase 1.55.0.
XDE VignetteUpdated 11 years ago

Robert Scharpf

Rendered from XDE.Rnw in XDE 2.53.0.
XdeParameterClass VignetteUpdated 11 years ago

Robert Scharpf

Rendered from XdeParameterClass.Rnw in XDE 2.53.0.
Basic GO UsageUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from GOusage.Rnw in annotate 1.85.0.
A New Interface to Plot Graphs Using RgraphvizUpdated 11 years ago

Kasper Daniel Hansen

Rendered from newRgraphvizInterface.Rnw in Rgraphviz 2.51.0.
How To Plot A Graph Using RgraphvizUpdated 11 years ago

Kasper Daniel Hansen

Rendered from Rgraphviz.Rnw in Rgraphviz 2.51.0.
PrimerUpdated 11 years ago

Stephen R. Piccolo

Rendered from SCAN.vignette.Rnw in SCAN.UPC 2.49.0.
ReportingTools basicsUpdated 11 years ago

Jason A. Hackney

Rendered from basicReportingTools.Rnw in ReportingTools 2.47.0.
ReportingTools shinyUpdated 11 years ago

Jason A. Hackney

Rendered from shiny.Rnw in ReportingTools 2.47.0.
runGCUpdated 11 years ago

Yann Guitton

Rendered from runGC.Rnw in metaMS 1.43.0.
Using MessinaUpdated 11 years ago

Mark Pinese

Rendered from messina.Rnw in messina 1.43.0.
INPower VignetteUpdated 11 years ago

Bill Wheeler

Rendered from vignette.Rnw in INPower 1.43.0.
ManualUpdated 11 years ago

Sander Bollen

Rendered from CAFE-manual.Rnw in CAFE 1.43.0.
An introduction to CNAnormUpdated 11 years ago

Stefano Berri

Rendered from CNAnorm.Snw in CNAnorm 1.53.0.
Using unifiedWMWqPCRUpdated 11 years ago

Joris Meys

Rendered from unifiedWMWqPCR.Rnw in unifiedWMWqPCR 1.43.0.
Trio Logic Regression and genotypic TDTUpdated 11 years ago

Holger Schwender

Rendered from trio.Rnw in trio 3.45.0.
Using geneRxClusterUpdated 11 years ago

Charles Berry

Rendered from tutorial.Rnw in geneRxCluster 1.43.0.
Analysing single-cell BS-Seq data with the "BEAT" packageUpdated 11 years ago

Kemal Akman

Rendered from BEAT.Rnw in BEAT 1.45.0.
Reverse-engineer transcriptional regulatory networks using qpgraphUpdated 11 years ago

Robert Castelo

Rendered from qpTxRegNet.Rnw in qpgraph 2.41.0.
lmdme: linear model framework for PCA/PLS analysis of ANOVA decomposition on Designed Multivariate Experiments in RUpdated 11 years ago

Cristobal Fresno

Rendered from lmdme-vignette.Rnw in lmdme 1.49.0.
msmsEDA: Batch effects detection in LC-MSMS experimentsUpdated 11 years ago

Josep Gregori

Rendered from msmsData-Vignette.Rnw in msmsEDA 1.45.0.
Testing and visualizing gene overlaps with the "GeneOverlap" packageUpdated 11 years ago

Ant

Rendered from GeneOverlap.Rnw in GeneOverlap 1.43.0.
How to use MiRaGE PackageUpdated 11 years ago

Y-h. Taguchi

Rendered from MiRaGE.Rnw in MiRaGE 1.49.0.
MineICA: Independent component analysis of genomic dataUpdated 11 years ago

Anne Biton

Rendered from MineICA.Rnw in MineICA 1.47.0.
metaSeqUpdated 11 years ago

Koki Tsuyuzaki

Rendered from metaSeq.Rnw in metaSeq 1.47.0.
Using omicade4Updated 11 years ago

Chen Meng

Rendered from omicade4.Rnw in omicade4 1.47.0.
HyperdrawUpdated 11 years ago

Paul Murrell

Rendered from hyperdraw.Rnw in hyperdraw 1.59.0.
An Introduction to the methylumi packageUpdated 11 years ago

Sean Davis

Rendered from methylumi.Rnw in methylumi 2.53.0.
Rmagpie ExamplesUpdated 11 years ago

Camille Maumet

Rendered from Magpie_examples.Rnw in Rmagpie 1.63.0.
msmsTests: controlling batch effects by blockingUpdated 11 years ago

Josep Gregori i Font

Rendered from msmsTests-Vignette2.Rnw in msmsTests 1.45.0.
msmsTests: post test filters to improve reproducibilityUpdated 11 years ago

Josep Gregori i Font

Rendered from msmsTests-Vignette.Rnw in msmsTests 1.45.0.
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence informationUpdated 11 years ago

Yue Li

Rendered from TargetScore.Rnw in TargetScore 1.45.0.
Quantify deregulation of pathways in cancerUpdated 11 years ago

Assif Yitzhaky

Rendered from Overview.Rnw in pathifier 1.45.0.
sSeqUpdated 11 years ago

Danni Yu

Rendered from sSeq.Rnw in sSeq 1.45.0.
Vignette for SPEMUpdated 11 years ago

Xinyi YANG

Rendered from SPEM-package.Rnw in SPEM 1.47.0.
An introduction to DriverNetUpdated 11 years ago

Jiarui Ding

Rendered from DriverNet-Overview.Rnw in DriverNet 1.47.0.
SNAGEE VignetteUpdated 11 years ago

David Venet

Rendered from SNAGEE.Rnw in SNAGEE 1.47.0.
DeconRNASeq DemoUpdated 11 years ago

Ting Gong

Rendered from DeconRNASeq.Rnw in DeconRNASeq 1.49.0.
ChIPXpressUpdated 11 years ago

George Wu

Rendered from ChIPXpress.Rnw in ChIPXpress 1.51.0.
An introduction to OSATUpdated 11 years ago

Li Yan

Rendered from OSAT.Rnw in OSAT 1.55.0.
Cancerclass: An R package for development and validation of diagnostic tests from high-dimensional molecular dataUpdated 11 years ago

Daniel Kosztyla

Rendered from vignette_cancerclass.Rnw in cancerclass 1.51.0.
iASeq VignetteUpdated 11 years ago

Yingying Wei

Rendered from iASeqVignette.Rnw in iASeq 1.51.0.
iBBiG User ManualUpdated 11 years ago

Aedin Culhane

Rendered from tutorial.Rnw in iBBiG 1.51.0.
Hybrid Multiple TestingUpdated 11 years ago

Demba Fofana

Rendered from HybridMTest.Rnw in HybridMTest 1.51.0.
coGPSUpdated 11 years ago

Yingying Wei

Rendered from coGPS.Rnw in coGPS 1.51.0.
Using AnimalUpdated 11 years ago

Wei Q. Deng

Rendered from GEWIST.rnw in GEWIST 1.51.0.
AffyRNADegradation ExampleUpdated 11 years ago

Mario Fasold

Rendered from vignette.Rnw in AffyRNADegradation 1.53.0.
Trigger TutorialUpdated 11 years ago

John D. Storey

Rendered from trigger.Rnw in trigger 1.53.0.
isobar for developersUpdated 11 years ago

Florian P Breitwieser

Rendered from isobar-devel.Rnw in isobar 1.53.0.
isobar for quantification of PTM datasetsUpdated 11 years ago

Florian P Breitwieser

Rendered from isobar-ptm.Rnw in isobar 1.53.0.
Part 0: Introduction and quick startUpdated 11 years ago

Michael Lawrence

Rendered from ggbio.Rnw in ggbio 1.55.0.
Sample cummeRbund workflowUpdated 11 years ago

Loyal A. Goff

Rendered from cummeRbund-example-workflow.Rnw in cummeRbund 2.49.0.
An introduction to AGDEXUpdated 11 years ago

Cuilan lani Gao

Rendered from AGDEX.rnw in AGDEX 1.55.0.
dksTutorialUpdated 11 years ago

Jeffrey T. Leek

Rendered from dks.Rnw in dks 1.53.0.
A guide to Dynamic Transcriptome Analysis (DTA)Updated 11 years ago

Bjoern Schwalb

Rendered from DTA.Rnw in DTA 2.53.0.
Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbationsUpdated 11 years ago

Xin Wang

Rendered from PANR-Vignette.Rnw in PANR 1.53.0.
Using weaver to process Sweave documentsUpdated 11 years ago

Seth Falcon

Rendered from weaver_howTo.Rnw in weaver 1.73.0.
GRENITSUpdated 11 years ago

Edward Morrissey

Rendered from GRENITS_package.Rnw in GRENITS 1.59.0.
Cormotif VignetteUpdated 11 years ago

Yingying Wei

Rendered from CormotifVignette.Rnw in Cormotif 1.53.0.
Using Repitools for Epigenomic Sequencing DataUpdated 11 years ago

Mark Robinson

Rendered from Repitools_vignette.Rnw in Repitools 1.53.0.
RCASPAR: Software for high-dimentional-data driven survival time predictionUpdated 11 years ago

Douaa Mugahid

Rendered from RCASPAR.Rnw in RCASPAR 1.53.0.
ANalysis Of Translational Activity (anota)Updated 11 years ago

Ola Larsson

Rendered from anota.Rnw in anota 1.55.0.
Plots with Embedded Tests for Gated Flow Cytometry DataUpdated 11 years ago

N. Hawkins

Rendered from flowPlots.Rnw in flowPlots 1.55.0.
ibhUpdated 11 years ago

Kircicegi Korkmaz

Rendered from ibh.Rnw in ibh 1.55.0.
snpMatrixUpdated 11 years ago

Hin-Tak Leung

Rendered from chopsticks-vignette.Rnw in chopsticks 1.73.0.
Overview of the mgsa package.Updated 11 years ago

Sebastian Bauer

Rendered from mgsa.Rnw in mgsa 1.55.0.
DEGraph: differential expression testing for gene networksUpdated 11 years ago

Laurent Jacob

Rendered from DEGraph.Rnw in DEGraph 1.59.0.
CRImage ManualUpdated 11 years ago

Henrik Failmezger

Rendered from CRImage.Rnw in CRImage 1.55.0.
A package for nonlinear dimension reduction with Isomap and LLE.Updated 11 years ago

Christoph Bartenhagen

Rendered from vignette.Rnw in RDRToolbox 1.57.0.
NTW vignetteUpdated 11 years ago

Yuanhua Liu

Rendered from NTW.Rnw in NTW 1.57.0.
affyILM1.3.0Updated 11 years ago

Myriam Kroll and Fabrice Berger

Rendered from affyILM.Rnw in affyILM 1.59.0.
flowTrans packageUpdated 11 years ago

Greg Finak

Rendered from flowTrans.Rnw in flowTrans 1.59.0.
add stuffUpdated 11 years ago

Wei Sun

Rendered from genoCN.Rnw in genoCN 1.59.0.
frmaTools: Create packages containing the vectors used by frma.Updated 11 years ago

Matthew N. McCall

Rendered from frmaTools.Rnw in frmaTools 1.59.0.
SpeCondUpdated 11 years ago

Florence Cavalli

Rendered from SpeCond.Rnw in SpeCond 1.61.0.
LiquidAssociation VignetteUpdated 11 years ago

Yen-Yi Ho

Rendered from LiquidAssociation.Rnw in LiquidAssociation 1.61.0.
Plotting expression data with ChromHeatMapUpdated 11 years ago

Tim F. Rayner

Rendered from ChromHeatMap.Rnw in ChromHeatMap 1.61.0.
CGHnormaliterUpdated 11 years ago

Bart P.P. van Houte

Rendered from CGHnormaliter.Rnw in CGHnormaliter 1.61.0.
Introduction to Data Analysis of the Roche xCELLigence System with RTCA PackageUpdated 11 years ago

Jitao David Zhang

Rendered from aboutRTCA.Rnw in RTCA 1.59.0.
RTCAtransformation: Discussion of transformation methods of RTCA dataUpdated 11 years ago

Jitao David Zhang

Rendered from RTCAtransformation.Rnw in RTCA 1.59.0.
AgiMicroRnaUpdated 11 years ago

Pedro Lopez-Romero

Rendered from AgiMicroRna.Rnw in AgiMicroRna 2.57.0.
Sample Size CalculationUpdated 11 years ago

Stephen Nyangoma

Rendered from clippda.Rnw in clippda 1.57.0.
MiChip miRNA Microarray ProcessingUpdated 11 years ago

Jonathon Blake

Rendered from MiChip.Rnw in MiChip 1.61.0.
Simulating ChIP-seq experimentsUpdated 11 years ago

Peter Humburg

Rendered from ChIPsimIntro.Rnw in ChIPsim 1.61.0.
Analyse RT-PCR data with the end-to-end script in ddCt packageUpdated 11 years ago

Jitao David Zhang

Rendered from rtPCR-usage.Rnw in ddCt 1.63.0.
BUS vignetteUpdated 11 years ago

Yuanhua Liu

Rendered from bus.rnw in BUS 1.63.0.
Fingerprinting for Flow CytometryUpdated 11 years ago

Herb Holyst

Rendered from flowFP_HowTo.Rnw in flowFP 1.65.0.
NCTools HowToUpdated 11 years ago

J. Zhang

Rendered from HowTo.Rnw in CNTools 1.63.0.
GeneRegionScanUpdated 11 years ago

Lasse Folkersen

Rendered from GeneRegionScan.Rnw in GeneRegionScan 1.63.0.
qPCR Normalization ExampleUpdated 11 years ago

Jessica Mar

Rendered from qpcrNorm.Rnw in qpcrNorm 1.65.0.
metahdep PrimerUpdated 11 years ago

John R. Stevens

Rendered from metahdep.Rnw in metahdep 1.65.0.
SPIAUpdated 11 years ago

Adi Laurentiu Tarca

Rendered from SPIA.Rnw in SPIA 2.59.0.
spkTools: Spike-in Data Analysis and VisualizationUpdated 11 years ago

Matthew N McCall

Rendered from spkDoc.Rnw in spkTools 1.63.0.
BicAREUpdated 11 years ago

Pierre Gestraud

Rendered from BicARE.Rnw in BicARE 1.65.0.
KCsmart example sessionUpdated 11 years ago

Jorma de Ronde

Rendered from KCS.Rnw in KCsmart 2.65.0.
MEDMEUpdated 11 years ago

Mattia Pelizzola

Rendered from MEDME.rnw in MEDME 1.67.0.
Howto: Discriminat Fuzzy PatternUpdated 11 years ago

Rodrigo Alvarez-Glez

Rendered from DFP.Rnw in DFP 1.65.0.
The Iterative Bayesian Model Averaging Algorithm For Survival AnalysisUpdated 11 years ago

Ka Yee Yeung

Rendered from iterativeBMAsurv.Rnw in iterativeBMAsurv 1.65.0.
ITALICSUpdated 11 years ago

Guillem Rigaill

Rendered from ITALICS.Rnw in ITALICS 2.67.0.
The Iterative Bayesian Model Averaging AlgorithmUpdated 11 years ago

Ka Yee Yeung

Rendered from iterativeBMA.Rnw in iterativeBMA 1.65.0.
An R Package for Estimating Gene Expressions using Multiple ScansUpdated 11 years ago

Mizanur Khondoker

Rendered from multiscan.Rnw in multiscan 1.67.0.
miRNApath: Pathway Enrichment for miRNA Expression DataUpdated 11 years ago

James M. Ward

Rendered from miRNApath.Rnw in miRNApath 1.67.0.
SIM vignetteUpdated 11 years ago

Renee X. de Menezes

Rendered from SIM.Rnw in SIM 1.77.0.
Primer Updated 11 years ago

Reid F. Thompson

Rendered from HELP.Rnw in HELP 1.65.0.
CMA ManualUpdated 11 years ago

Roman Hornung

Rendered from CMA_vignette.rnw in CMA 1.65.0.
CGHcallUpdated 11 years ago

Sjoerd Vosse

Rendered from CGHregions.Rnw in CGHregions 1.65.0.
RBioinf IntroductionUpdated 11 years ago

Robert Gentleman

Rendered from RBioinf.Rnw in RBioinf 1.67.0.
Linear models in GSEAUpdated 11 years ago

Assaf Oron

Rendered from GSEAlm.Rnw in GSEAlm 1.67.0.
Imputation and meta-analysisUpdated 11 years ago

David Clayton

Rendered from imputation-vignette.Rnw in snpStats 1.57.0.
LD statisticsUpdated 11 years ago

David Clayton

Rendered from ld-vignette.Rnw in snpStats 1.57.0.
snpMatrix-differencesUpdated 11 years ago

David Clayton

Rendered from differences.Rnw in snpStats 1.57.0.
snpStats introductionUpdated 11 years ago

David Clayton

Rendered from snpStats-vignette.Rnw in snpStats 1.57.0.
TDT testsUpdated 11 years ago

David Clayton

Rendered from tdt-vignette.Rnw in snpStats 1.57.0.
BCRANKUpdated 11 years ago

Adam Ameur

Rendered from BCRANK.Rnw in BCRANK 1.69.0.
Introduction to MDQCUpdated 11 years ago

Gabriela Cohen-Freue

Rendered from mdqcvignette.Rnw in mdqc 1.69.0.
GraphAlignmentUpdated 11 years ago

Joern P. Meier

Rendered from GraphAlignment.Rnw in GraphAlignment 1.71.0.
Manual for the gaga libraryUpdated 11 years ago

David Rossell

Rendered from gagamanual.Rnw in gaga 2.53.0.
RtreemixUpdated 11 years ago

Jasmina Bogojeska

Rendered from Rtreemix.Rnw in Rtreemix 1.69.0.
CGHcallUpdated 11 years ago

Mark van de Wiel

Rendered from CGHcall.Rnw in CGHcall 2.69.0.
vbmp TutorialUpdated 11 years ago

Nicola Lama

Rendered from vbmp.Rnw in vbmp 1.75.0.
Examples of plotting graphs Using RgraphvizUpdated 11 years ago

Florian Hahne

Rendered from biocGraph.Rnw in biocGraph 1.69.0.
HOWTO layout pathwaysUpdated 11 years ago

Florian Hahne

Rendered from layingOutPathways.Rnw in biocGraph 1.69.0.
Calculation of genetic relatedness/relationship between individuals in the pedigreeUpdated 11 years ago

David Henderson

Rendered from geneticRelatedness.Rnw in GeneticsPed 1.69.0.
Pedigree handlingUpdated 11 years ago

David Henderson

Rendered from pedigreeHandling.Rnw in GeneticsPed 1.69.0.
Quantitative genetic (animal) model example in RUpdated 11 years ago

David Henderson

Rendered from quanGenAnimalModel.Rnw in GeneticsPed 1.69.0.
ACMEUpdated 11 years ago

Sean Davis

Rendered from ACME.Rnw in ACME 2.63.0.
SLqPCRUpdated 11 years ago

Matthias Kohl

Rendered from SLqPCR.Rnw in SLqPCR 1.73.0.
BufferedMatrix: IntroductionUpdated 11 years ago

Ben Bolstad

Rendered from BufferedMatrix.Rnw in BufferedMatrix 1.71.0.
Building Annotation Packages with pdInfoBuilder for Use with the oligo PackageUpdated 11 years ago

Benilton Carvalho

Rendered from BuildingPDInfoPkgs.Rnw in pdInfoBuilder 1.71.0.
PDInfo Package Building Affymetrix Mapping ChipsUpdated 11 years ago

Benilton Carvalho

Rendered from howto-AffymetrixMapping.Rnw in pdInfoBuilder 1.71.0.
occugeneUpdated 11 years ago

Oliver Will

Rendered from occugene.Rnw in occugene 1.67.0.
RbcBook1 PrimerUpdated 11 years ago

Vince Carey

Rendered from RbcBook1.Rnw in RbcBook1 1.75.0.
BioMVCClassUpdated 11 years ago

Elizabeth Whalen

Rendered from BioMVCClass.Rnw in BioMVCClass 1.75.0.
spikeLIUpdated 11 years ago

Enrico Carlon

Rendered from spikeLI.Rnw in spikeLI 2.67.0.
quantsmoothUpdated 11 years ago

Jan Oosting

Rendered from quantsmooth.Rnw in quantsmooth 1.73.0.
HarshlightUpdated 11 years ago

Maurizio Pellegrino

Rendered from Harshlight.Rnw in Harshlight 1.79.0.
ABarray gene expressionUpdated 11 years ago

Yongming Andrew Sun

Rendered from ABarray.Rnw in ABarray 1.75.0.
ABarray gene expression GUI interfaceUpdated 11 years ago

Yongming Andrew Sun

Rendered from ABarrayGUI.Rnw in ABarray 1.75.0.
cghMCR findMCRUpdated 11 years ago

J. Zhang

Rendered from findMCR.Rnw in cghMCR 1.65.0.
maCorrPlot IntroductionUpdated 11 years ago

Alexander Ploner

Rendered from maCorrPlot.Rnw in maCorrPlot 1.77.0.
Sample Size and Power Calculation in Microarray Studies Using the \Rpackage{sizepower} packageUpdated 11 years ago

Weiliang Qiu

Rendered from sizepower.Rnw in sizepower 1.77.0.
Annotation-Driven ClusteringUpdated 11 years ago

Claudio Lottaz

Rendered from tr_2005_02.Rnw in adSplit 1.77.0.
pathRender overviewUpdated 11 years ago

Vince Carey

Rendered from pathRender.Rnw in pathRender 1.75.0.
pathway graphs colored by expression mapUpdated 11 years ago

Vince Carey

Rendered from plotExG.Rnw in pathRender 1.75.0.
gene presence/absence callsUpdated 11 years ago

Peter Warren

Rendered from panp.Rnw in panp 1.77.0.
MantelCorrVignetteUpdated 11 years ago

Brian Steinmeyer

Rendered from MantelCorrVignette.Rnw in MantelCorr 1.77.0.
RLMM DocUpdated 11 years ago

Nusrat Rabbee

Rendered from RLMM.Rnw in RLMM 1.69.0.
GlobalAncovaDecompUpdated 11 years ago

Manuela Hummel

Rendered from GlobalAncovaDecomp.rnw in GlobalAncova 4.25.0.
timecourse manualUpdated 11 years ago

Yu Chuan Tai

Rendered from timecourse.Rnw in timecourse 1.79.0.
Documentation on diffGeneAnalysisUpdated 11 years ago

Choudary Jagarlamudi

Rendered from diffGeneAnalysis.Rnw in diffGeneAnalysis 1.89.0.
Annotation OverviewUpdated 11 years ago

Effi Kenigsberg

Rendered from fdrame.Rnw in fdrame 1.79.0.
Sample Size Estimation for Microarray Experiments Using the \code{ssize} packageUpdated 11 years ago

Gregory R. Warnes

Rendered from ssize.Rnw in ssize 1.81.0.
Using the geneRecommender PackageUpdated 11 years ago

Greg Hather

Rendered from geneRecommender.Rnw in geneRecommender 1.79.0.
HOWTO: idiogramUpdated 11 years ago

Karl J. Dykema

Rendered from idiogram.Rnw in idiogram 1.83.0.
MiPP OverviewUpdated 11 years ago

Sukwoo Kim

Rendered from MiPP.Rnw in MiPP 1.79.0.
apComplexUpdated 11 years ago

Denise Scholtens

Rendered from apComplex.Rnw in apComplex 2.73.0.
SAGEnhaftUpdated 11 years ago

Tim Beissbarth

Rendered from SAGEnhaft.Rnw in sagenhaft 1.77.0.
Quick intro to SBMLRUpdated 11 years ago

Tomas Radivoyevitch

Rendered from quick-start.Rnw in SBMLR 2.3.0.
MVCClassUpdated 11 years ago

Elizabeth Whalen

Rendered from MVCClass.Rnw in MVCClass 1.81.0.
hopachUpdated 11 years ago

Katherine S. Pollard

Rendered from hopach.Rnw in hopach 2.67.0.
genAriseGUI VignetteUpdated 11 years ago

IFC Development Team

Rendered from genArise.Rnw in genArise 1.83.0.
nnNorm TutorialUpdated 11 years ago

Adi Laurentiu Tarca

Rendered from nnNorm.Rnw in nnNorm 2.71.0.
MLInterfaces Computer ClusterUpdated 11 years ago

Vincent Carey

Rendered from xvalComputerClusters.Rnw in MLInterfaces 1.87.0.
HEM OverviewUpdated 11 years ago

HyungJun Cho

Rendered from HEM.Rnw in HEM 1.79.0.
aCGH OverviewUpdated 11 years ago

Peter Dimitrov

Rendered from aCGH.Rnw in aCGH 1.85.0.
DNAcopyUpdated 11 years ago

Venkatraman E. Seshan

Rendered from DNAcopy.Rnw in DNAcopy 1.81.0.
Converting Between Microarray Data ClassesUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from convert.Rnw in convert 1.83.0.
marray NormalizationUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marrayNorm.Rnw in marray 1.85.0.
marray OverviewUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marray.Rnw in marray 1.85.0.
marrayClasses OverviewUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marrayClasses.Rnw in marray 1.85.0.
marrayClasses Tutorial (short)Updated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marrayClassesShort.Rnw in marray 1.85.0.
marrayInput IntroductionUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marrayInput.Rnw in marray 1.85.0.
marrayPlots OverviewUpdated 11 years ago

Yee Hwa (Jean) Yang

Rendered from marrayPlots.Rnw in marray 1.85.0.
Extracting limma objects from limmaGUI filesUpdated 11 years ago

Gordon Smyth

Rendered from extract.Rnw in limmaGUI 1.83.0.
limmaGUI VignetteUpdated 11 years ago

Gordon Smyth

Rendered from limmaGUI.Rnw in limmaGUI 1.83.0.
affylmGUI VignetteUpdated 11 years ago

Gordon Smyth

Rendered from affylmGUI.Rnw in affylmGUI 1.81.0.
Extracting affy and limma objects from affylmGUI filesUpdated 11 years ago

Gordon Smyth

Rendered from extract.Rnw in affylmGUI 1.81.0.
goTools overviewUpdated 11 years ago

Agnes Paquet

Rendered from goTools.Rnw in goTools 1.81.0.
altcdfenvsUpdated 11 years ago

Laurent Gautier

Rendered from altcdfenvs.Rnw in altcdfenvs 2.69.0.
HOWTO PROcessUpdated 11 years ago

Xiaochun Li

Rendered from howtoprocess.Rnw in PROcess 1.83.0.
Introduction to EBarraysUpdated 11 years ago

Ming Yuan

Rendered from vignette.Rnw in EBarrays 2.71.0.
A short presentation of the basic classes defined in Biostrings 2Updated 11 years ago

Hervé Pagès

Rendered from Biostrings2Classes.Rnw in Biostrings 2.75.1.
Adaptive Gene Picking for Microarray Expression Data AnalysisUpdated 11 years ago

Brian S. Yandell

Rendered from pickgene.Rnw in pickgene 1.79.0.
LPE test for microarray data with small number of replicatesUpdated 11 years ago

Nitin Jain

Rendered from LPE.Rnw in LPE 1.81.0.
webbioc Demo ScriptUpdated 11 years ago

Colin A. Smith

Rendered from demoscript.Rnw in webbioc 1.79.0.
webbioc OverviewUpdated 11 years ago

Colin A. Smith

Rendered from webbioc.Rnw in webbioc 1.79.0.
factDesignUpdated 11 years ago

Denise Scholtens

Rendered from factDesign.Rnw in factDesign 1.83.0.
MeasurementError.cor TutorialUpdated 11 years ago

Beiying Ding

Rendered from MeasurementError.cor.Rnw in MeasurementError.cor 1.79.0.
siggenes ManualUpdated 11 years ago

Holger Schwender

Rendered from siggenes.Rnw in siggenes 1.81.0.
gcrma1.2Updated 11 years ago

Z. Wu

Rendered from gcrma2.0.Rnw in gcrma 2.79.0.
affycomp primerUpdated 11 years ago

Robert D. Shear

Rendered from affycomp.Rnw in affycomp 1.83.0.
widgetTools IntroductionUpdated 11 years ago

Jianhua Zhang

Rendered from widgetTools.Rnw in widgetTools 1.85.0.
tkWidgets contentsUpdated 11 years ago

J. Zhang

Rendered from tkWidgets.Rnw in tkWidgets 1.85.0.
tkWidgets importWizardUpdated 11 years ago

J. Zhang

Rendered from importWizard.Rnw in tkWidgets 1.85.0.
Introduction to ctcUpdated 11 years ago

Antoine Lucas

Rendered from ctc.Rnw in ctc 1.81.0.
snm TutorialUpdated 11 years ago

John D. Storey

Rendered from snm.Rnw in snm 1.55.0.
TurboNorm OverviewUpdated 11 years ago

Maarten van Iterson

Rendered from turbonorm.Rnw in TurboNorm 1.55.0.
GeneMeta VignetteUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from GeneMeta.Rnw in GeneMeta 1.79.0.
bioDist IntroductionUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from bioDist.Rnw in bioDist 1.79.0.
gpls TutorialUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from gpls.Rnw in gpls 1.79.0.
Visualization of Microarray DataUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from visualize.Rnw in geneplotter 1.85.0.
Annotation OverviewUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from annotate.Rnw in annotate 1.85.0.
HowTo: Get HTML OutputUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from prettyOutput.Rnw in annotate 1.85.0.
Using Affymetrix Probe Level DataUpdated 11 years ago

Bioconductor Package Maintainer

Rendered from useProbeInfo.Rnw in annotate 1.85.0.
Introduction to the plotAlongChrom functionUpdated 11 years ago

Zhenyu Xu

Rendered from plotAlongChrom.Rnw in tilingArray 1.85.0.
Introduction to using the segment function to fit a piecewise constant curveUpdated 11 years ago

Zhenyu Xu

Rendered from findsegments.Rnw in tilingArray 1.85.0.
Normalisation with the normalizeByReference function in the tilingArray packageUpdated 11 years ago

Zhenyu Xu

Rendered from assessNorm.Rnw in tilingArray 1.85.0.
Segmentation demoUpdated 11 years ago

Zhenyu Xu

Rendered from segmentation.Rnw in tilingArray 1.85.0.
Supplement. Calculation of the cost matrixUpdated 11 years ago

Zhenyu Xu

Rendered from costMatrix.Rnw in tilingArray 1.85.0.
Introduction to rTRMuiUpdated 11 years ago

Diego Diez

Rendered from rTRMui.Rnw in rTRMui 1.45.0.
Codelink IntructionUpdated 11 years ago

Diego Diez

Rendered from Codelink_Introduction.Rnw in codelink 1.75.0.
Codelink LegacyUpdated 11 years ago

Diego Diez

Rendered from Codelink_Legacy.Rnw in codelink 1.75.0.
copa OverviewUpdated 11 years ago

James W. MacDonald

Rendered from copa.Rnw in copa 1.75.0.
clusterStab OverviewUpdated 11 years ago

James W. MacDonald

Rendered from clusterStab.Rnw in clusterStab 1.79.0.
makecdfenv primerUpdated 11 years ago

James W. MacDonald

Rendered from makecdfenv.Rnw in makecdfenv 1.83.0.
Quick start for rsbmlUpdated 11 years ago

Michael Lawrence

Rendered from quick-start.Rnw in rsbml 2.65.0.
lapmix exampleUpdated 11 years ago

Yann Ruffieux

Rendered from lapmix-example.Rnw in lapmix 1.73.0.
keggorthology overviewUpdated 11 years ago

VJ Carey

Rendered from keggorth.Rnw in keggorthology 2.59.0.
Analysing RNA-Seq data with the "BADER" packageUpdated 11 years ago

Andreas Neudecker

Rendered from BADER.Rnw in BADER 1.45.0.
Introduction to the les package: Identifying Differential Effects in Tiling Microarray Data with the Loci of Enhanced Significance FrameworkUpdated 11 years ago

Julian Gehring

Rendered from les.Rnw in les 1.57.0.
An R package for detecting low frequency variants in deep sequencing experimentsUpdated 11 years ago

Moritz Gerstung

Rendered from deepSNV.Rnw in deepSNV 1.53.0.
Using paircompvizUpdated 11 years ago

Michal Burda

Rendered from vignette.Rnw in paircompviz 1.45.0.
hapFabia: Manual for the R packageUpdated 11 years ago

Andreas Mitterecker

Rendered from hapfabia.Rnw in hapFabia 1.49.0.
Analysis of Flow Cytometry Bead DataUpdated 11 years ago

Nikolas Pontikos

Rendered from HowTo-flowBeads.Rnw in flowBeads 1.45.0.
Introduction to antiProfilesUpdated 12 years ago

Hector Corrada Bravo

Rendered from antiProfiles.Rnw in antiProfiles 1.47.0.
RNAseq samplesizeUpdated 12 years ago

Terry M Therneau

Rendered from samplesize.Rnw in RNASeqPower 1.47.0.
ARRmNormalizationUpdated 12 years ago

Jean-Philippe Fortin

Rendered from ARRmNormalization.Rnw in ARRmNormalization 1.47.0.
An introduction to PLGEMUpdated 12 years ago

Norman Pavelka

Rendered from plgem.Rnw in plgem 1.79.0.
Missing value imputationUpdated 12 years ago

Henning Redestig

Rendered from missingValues.Rnw in pcaMethods 1.99.0.
Introduction to the GSRI package: Estimating Regulatory Effects utilizing the Gene Set Regulation IndexUpdated 13 years ago

Julian Gehring

Rendered from gsri.Rnw in GSRI 2.55.0.