rgsepd

DOI: 10.18129/B9.bioc.rgsepd    

Gene Set Enrichment / Projection Displays

Bioconductor version: Release (3.6)

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq 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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rgsepd")

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		NEWS

Details

biocViews	DifferentialExpression, GeneSetEnrichment, RNASeq, Software
Version	1.10.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	GPL-3
Depends	R (>= 3.3.0), DESeq2, goseq(>= 1.17)
Imports	gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, hash, AnnotationDbi
LinkingTo
Suggests	boot, tools, RUnit, BiocGenerics, knitr, xtable
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	rgsepd_1.10.0.tar.gz
Windows Binary	rgsepd_1.10.0.zip
Mac OS X 10.11 (El Capitan)	rgsepd_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rgsepd
Package Short Url	http://bioconductor.org/packages/rgsepd/
Package Downloads Report	Download Stats