To install this package, start R and enter:

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

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

SeqGSEA

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see SeqGSEA.

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Bioconductor version: 2.12

The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.

Author: Xi Wang <Xi.Wang at newcastle.edu.au>

Maintainer: Xi Wang <Xi.Wang at newcastle.edu.au>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("SeqGSEA")

PDF	R Script	Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package
PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, HighThroughputSequencing, RNAseq, Software
Version	1.0.2
In Bioconductor since	BioC 2.12 (R-3.0) (3 years)
License	GPL (>= 3)
Depends	Biobase, DESeq, biomaRt, foreach
Imports	methods, doParallel
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Depends On Me
Imports Me
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Build Report

Package Archives

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

Package Source	SeqGSEA_1.0.2.tar.gz
Windows Binary	SeqGSEA_1.0.2.zip
Mac OS X 10.6 (Snow Leopard)	SeqGSEA_1.0.2.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/SeqGSEA/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/SeqGSEA/
Package Downloads Report	Download Stats

Documentation »

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