rgsepd

DOI: 10.18129/B9.bioc.rgsepd    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see rgsepd.

Gene Set Enrichment / Projection Displays

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

PDF	R Script	An Introduction to the rgsepd package
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software
Version	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	GPL-3
Depends	R (>= 4.2.0), DESeq2, goseq(>= 1.28)
Imports	gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi
LinkingTo
Suggests	boot, tools, BiocGenerics, knitr, xtable
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	rgsepd_1.28.0.tar.gz
Windows Binary	rgsepd_1.28.0.zip
macOS Binary (x86_64)	rgsepd_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rgsepd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rgsepd
Package Short Url	https://bioconductor.org/packages/rgsepd/
Package Downloads Report	Download Stats