source("http://bioconductor.org/biocLite.R")
biocLite("SeqGSEA")

SeqGSEA

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

Bioconductor version: 2.13

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 mdc-berlin.de>

Installation

To install this package, start R and enter:

source("http://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
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, HighThroughputSequencing, RNAseq, Software
Version	1.2.1
In Bioconductor since	BioC 2.12 (R-3.0)
License	GPL (>= 3)
Depends	Biobase, BiocGenerics, DESeq, biomaRt, foreach
Imports	methods, doParallel
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Package Archives

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

Package Source	SeqGSEA_1.2.1.tar.gz
Windows Binary	SeqGSEA_1.2.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	SeqGSEA_1.2.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats