Package: OSCA.workflows 1.21.0

Peter Hickey

OSCA.workflows: OSCA Workflows

Deploys the workflows of the "Orchestrating Single Cell Analysis with Bioconductor" book. This contains worked case studies of analyses of a variety of single-cell datasets, each proceeding from a SingleCellExperiment object. Exposition is generally minimal other than for dataset-specific justifications for parameter tweaks; refer to the other books in the OCSA collection for a detailed explanation of the theoretical basis of each step. It is intended for readers who already know the background and just want some code to copy and paste into their own analyses.

Authors:Robert Amezquita [aut], Aaron Lun [aut], Stephanie Hicks [aut], Raphael Gottardo [aut], Peter Hickey [cre]

OSCA.workflows_1.21.0.tar.gz
OSCA.workflows_1.21.0.tar.gz(r-4.7-any)OSCA.workflows_1.21.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OSCA.workflows/json (API)

# Install 'OSCA.workflows' in R:
install.packages('OSCA.workflows', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/osca-source/osca.workflows/issues

On BioConductor:OSCA.workflows-1.21.0(books 3.24)OSCA.workflows-1.20.0(books 3.23)

immunooncologyworkflowworkflowsinglecellworkflowdatapkg

4.95 score 4 stars 1 packages 0 exports 207 dependencies

Last updated from:b4be006c21. Checks:1 NOTE, 2 WARNING, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE288
linux-develWARNING493
source / vignettesERROR473
linux-releaseWARNING418

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seAnnotationDbiAnnotationFilterAnnotationHubaskpassassertthatassortheadbase64encbatchelorbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStyleBiocVersionBiostringsbitbit64bitopsblobblusterbookdownbslibcachemcelldexcigarillocliclusterCodeDependscodetoolscoopcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydplyrdqrngDropletTestFilesDropletUtilsdynamicTreeCutedgeRelasticnetEnsDb.Hsapiens.v86ensembldbevaluateExperimentHubfarverfastmapfilelockFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggplot2ggrepelglobalsgluegraphgridExtragtablegypsumh5mreadHCADataHDF5Arrayhighrhtmltoolshttrhttr2igraphIRangesirlbaisobandjquerylibjsonlitejsonvalidateKEGGRESTkernlabknitrlabelinglambda.rlarslatticelazyevallifecyclelimmalistenvlocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeopensslorg.Hs.eg.dborg.Mm.eg.dborigamiparallellypheatmappillarpkgconfigpngProtGenericspurrrR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlRdpackrebookResidualMatrixrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscPCAscranscRNAseqscuttleSeqinfoSingleCellExperimentSingleRsitmosnowSparseArraysparseMatrixStatssparsepcastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8uwotV8vctrsviporviridisviridisLitewithrxfunXMLXVectoryaml