rgsepd

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

Gene Set Enrichment / Projection Displays

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DOI: 10.18129/B9.bioc.rgsepd

Bioconductor version: Development (3.23)

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 "4.6") 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")

An Introduction to the rgsepd package PDF R Script

Reference Manual PDF

README Text

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software

Version 1.43.0

In Bioconductor since BioC 3.1 (R-3.2) (10.5 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

Suggests boot, tools, BiocGenerics, knitr, xtable

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Build Report Build Report

Package Archives

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

Source Package rgsepd_1.43.0.tar.gz

Windows Binary (x86_64) rgsepd_1.43.0.zip

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/rgsepd

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rgsepd

Bioc Package Browser https://code.bioconductor.org/browse/rgsepd/

Package Short Url https://bioconductor.org/packages/rgsepd/

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