ReactomePA

This is the development version of ReactomePA; for the stable release version, see ReactomePA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

Reactome Pathway Analysis

Bioconductor version: Development (3.24)

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis, network-based enrichment analysis (NSEA) on the Reactome reaction graph, Bayesian term selection, weighted enrichment, and several functions for visualization. This package is not affiliated with the Reactome team.

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

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Guangchuang Yu. ReactomePA: Reactome Pathway Analysis. doi:10.18129/B9.bioc.ReactomePA, R package version 1.99.2, https://bioconductor.org/packages/ReactomePA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("ReactomePA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("ReactomePA")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization
Version	1.99.2
In Bioconductor since	BioC 2.10 (R-2.15) (14.5 years)
License	GPL-2
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, enrichplot, enrichit (>= 0.2.2), ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson, Matrix, utils, yulab.utils (>= 0.1.5)
System Requirements
URL	https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/GuangchuangYu/ReactomePA/issues

Suggests	clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat
Linking To
Enhances
Depends On Me	maEndToEnd
Imports Me	bioCancer, ExpHunterSuite, famat, gINTomics, miRSM, miRspongeR, mitology, Pigengene, scTensor
Suggests Me	CBNplot, ChIPseeker, cola, epiSeeker, GeDi, GRaNIE, scGPS, scGraphVerse, XYomics
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ReactomePA_1.99.2.tar.gz
Windows Binary (x86_64)	ReactomePA_1.99.2.zip
macOS Binary (big-sur-x86_64)	ReactomePA_1.99.2.tgz
macOS Binary (sonoma-arm64)	ReactomePA_1.99.2.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	https://bioconductor.org/packages/ReactomePA/
Package Downloads Report	Download Stats