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Bioconductor - rgsepd (development version)

rgsepd

This is the development version of rgsepd; for the stable release version, see rgsepd.

Gene Set Enrichment / Projection Displays

Bioconductor version: Development (3.22)

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Author: Karl Stamm

Maintainer: Karl Stamm <karl.stamm at gmail.com>

Citation (from within R, enter citation("rgsepd")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rgsepd")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rgsepd")
Details biocViews DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software Version 1.41.0 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License GPL-3 Depends R (>= 4.2.0), DESeq2, goseq(>= 1.28) Imports gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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