ReactomePA

DOI: 10.18129/B9.bioc.ReactomePA    

Reactome Pathway Analysis

Bioconductor version: Release (3.8)

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

Author: Guangchuang Yu [aut, cre], Vladislav Petyuk [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ReactomePA", version = "3.8")

Documentation

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

browseVignettes("ReactomePA")

 

HTML R Script An R package for Reactome Pathway Analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization
Version 1.26.0
In Bioconductor since BioC 2.10 (R-2.15) (6.5 years)
License GPL-2
Depends R (>= 3.4.0)
Imports AnnotationDbi, DOSE(>= 3.5.1), enrichplot, ggplot2, ggraph, reactome.db, igraph, graphite
LinkingTo
Suggests BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc, testthat
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/software/ReactomePA
BugReports https://github.com/GuangchuangYu/ReactomePA/issues
Depends On Me maEndToEnd
Imports Me bioCancer, LINC, miRsponge
Suggests Me ChIPseeker, CINdex, clusterProfiler
Links To Me
Build Report  

Package Archives

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

Source Package ReactomePA_1.26.0.tar.gz
Windows Binary ReactomePA_1.26.0.zip
Mac OS X 10.11 (El Capitan) ReactomePA_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ReactomePA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReactomePA
Package Short Url http://bioconductor.org/packages/ReactomePA/
Package Downloads Report Download Stats

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