To install this package, start R and enter:

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

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

ReactomePA

   

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

Reactome Pathway Analysis

Bioconductor version: 2.12

This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection.

Author: Guangchuang Yu <guangchuangyu at gmail.com>

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("ReactomePA")

 

PDF R Script An introduction to ReactomePA
PDF cnetplot.pdf
PDF rPAclusterProfiler.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Bioinformatics, Pathways, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 2.10 (R-2.15) (4 years)
License GPL-2
Depends R (>= 2.10), DOSE
Imports methods, AnnotationDbi, reactome.db, org.Hs.eg.db, stats4, plyr, igraph, qvalue, graphics
LinkingTo
Suggests clusterProfiler, GOSemSim, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me clusterProfiler, DOSE
Build Report  

Package Archives

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

Package Source ReactomePA_1.4.0.tar.gz
Windows Binary ReactomePA_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) ReactomePA_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ReactomePA/tree/release-2.12
Package Short Url http://bioconductor.org/packages/ReactomePA/
Package Downloads Report Download Stats

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