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roastgsa

Rotation based gene set analysis

Bioconductor version: 3.23 · Package version: 1.10.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("roastgsa")

Details

MaintainerAdria Caballe <adria.caballe@irbbarcelona.org>
AuthorAdria Caballe [aut, cre] (ORCID: <https://orcid.org/0000-0002-2388-4713>)
LicenseGPL-3
Bug Reportshttps://github.com/adricaba/roastgsa/issues
Downloads rank202
Source branchRELEASE_3_23
biocViewsAlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, Cheminformatics, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, Epigenetics, ExonArray, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Metabolomics, MicroRNAArray, Microarray, MultipleComparison, Normalization, OneChannel, Pathways, Preprocessing, ProprietaryPlatforms, Proteomics, QualityControl, RNASeq, Regression, Sequencing, Software, Survival, SystemsBiology, TimeCourse, Transcription, Transcriptomics, TwoChannel, mRNAMicroarray

Documentation

Download

Dependencies

Depends: R (>= 4.3.0)

Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase

Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2