Package: roastgsa 1.11.0

Adria Caballe

roastgsa: Rotation based gene set analysis

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

Authors:Adria Caballe [aut, cre]

roastgsa_1.11.0.tar.gz
roastgsa_1.11.0.zip(r-4.7)roastgsa_1.11.0.zip(r-4.6)roastgsa_1.11.0.zip(r-4.5)
roastgsa_1.11.0.tgz(r-4.6-any)roastgsa_1.11.0.tgz(r-4.5-any)
roastgsa_1.11.0.tar.gz(r-4.7-any)roastgsa_1.11.0.tar.gz(r-4.6-any)
roastgsa_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
roastgsa/json (API)

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

Bug tracker:https://github.com/adricaba/roastgsa/issues

Datasets:

On BioConductor:roastgsa-1.11.0(bioc 3.24)roastgsa-1.10.0(bioc 3.23)

microarraypreprocessingnormalizationgeneexpressionsurvivaltranscriptionsequencingtranscriptomicsbayesianclusteringregressionrnaseqmicrornaarraymrnamicroarrayfunctionalgenomicssystemsbiologyimmunooncologydifferentialexpressiongenesetenrichmentbatcheffectmultiplecomparisonqualitycontroltimecoursemetabolomicsproteomicsepigeneticscheminformaticsexonarrayonechanneltwochannelproprietaryplatformscellbiologybiomedicalinformaticsalternativesplicingdifferentialsplicingdataimportpathways

3.89 score 13 scripts 8 exports 27 dependencies

Last updated from:095e6cc764. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE232
linux-devel-x86_64NOTE333
source / vignettesOK327
linux-release-x86_64NOTE264
macos-release-arm64NOTE127
macos-oldrel-arm64NOTE122
windows-develNOTE172
windows-releaseNOTE257
windows-oldrelNOTE183
wasm-releaseOK225

Exports:heatmaprgsa_hmhtmlrgsaploteffsignaturesizeplotGSEAplotStatsroastgsassGSAvarrotrand

Dependencies:BiobaseBiocGenericsbitopscaToolsclicpp11farvergenericsggplot2gluegplotsgtablegtoolsisobandKernSmoothlabelinglifecyclelimmaR6RColorBrewerrlangS7scalesstatmodvctrsviridisLitewithr

roastgsa vignette (gene set collections)
Installation | Using gene set collections for battery testing | Gene set collections | Usage of Hallmarks in another example with real data | sessionInfo | References
Rendered fromroastgsaExample_genesetcollections.Rmdusingknitr::rmarkdown

Last update: 2023-08-15
Started: 2023-07-19

roastgsa vignette (main)
Installation | Paper associated to R package | Data: array experiment from GSEABenchmarkeR | Gene set enrichment analysis using roastgsa | Data treatment | Model setting | Visualization of the results | Effective signature size | Functions to present the results | Single sample GSA | sessionInfo | References
Rendered fromroastgsaExample_main.Rmdusingknitr::rmarkdown

Last update: 2023-08-15
Started: 2023-07-19

roastgsa vignette (RNAseq)
Installation | roastgsa in RNA-seq data | Data: RNA-seq experiment from GSEABenchmarkeR | Data normalization and filtering | Gene sets | Enrichment analysis | Visualization of the results | sessionInfo | References
Rendered fromroastgsaExample_RNAseq.Rmdusingknitr::rmarkdown

Last update: 2023-08-15
Started: 2023-07-19