SeqGSEA

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("SeqGSEA")

Documentation

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, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>= 3)
Depends Biobase, doParallel, DESeq
Imports methods, biomaRt
Suggests easyRNASeq, GenomicRanges
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source SeqGSEA_1.4.0.tar.gz
Windows Binary SeqGSEA_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SeqGSEA_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center