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Bioconductor - ReactomePA

ReactomePA

This is the released version of ReactomePA; for the devel version, see ReactomePA.

Reactome Pathway Analysis

Bioconductor version: Release (3.21)

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. 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")): Installation

To install this package, start R (version "4.5") and enter:


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

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")
Details biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization Version 1.52.0 In Bioconductor since BioC 2.10 (R-2.15) (13.5 years) License GPL-2 Depends R (>= 3.4.0) Imports AnnotationDbi, DOSE(>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson, yulab.utils (>= 0.1.5) System Requirements URL https://yulab-smu.top/contribution-knowledge-mining/ Bug Reports https://github.com/GuangchuangYu/ReactomePA/issues See More Suggests BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat Linking To Enhances Depends On Me maEndToEnd Imports Me bioCancer, gINTomics, miRSM, miRspongeR, Pigengene, scTensor, ExpHunterSuite Suggests Me CBNplot, ChIPseeker, CINdex, cola, GeDi, GRaNIE, scGPS Links To Me Build Report Build Report Package Archives

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

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