To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

rgsepd

 

Gene Set Enrichment / Projection Displays

Bioconductor version: Release (3.5)

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>

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

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 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 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.

Package Source rgsepd_1.8.0.tar.gz
Windows Binary rgsepd_1.8.0.zip
Mac OS X 10.11 (El Capitan) rgsepd_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rgsepd
Package Short Url http://bioconductor.org/packages/rgsepd/
Package Downloads Report Download Stats

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