Package: ReactomePA 1.99.2

Guangchuang Yu

ReactomePA: Reactome Pathway Analysis

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.

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

ReactomePA_1.99.2.tar.gz
ReactomePA_1.99.2.zip(r-4.7-any)ReactomePA_1.99.2.zip(r-4.6-any)ReactomePA_1.99.2.zip(r-4.5-any)
ReactomePA_1.99.2.tgz(r-4.6-any)ReactomePA_1.99.2.tgz(r-4.5-any)
ReactomePA_1.99.2.tar.gz(r-4.7-any)ReactomePA_1.99.2.tar.gz(r-4.6-any)
ReactomePA_1.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReactomePA/json (API)

# Install 'ReactomePA' in R:

install.packages('ReactomePA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guangchuangyu/reactomepa/issues

On BioConductor:ReactomePA-1.57.0(bioc 3.24)ReactomePA-1.56.0(bioc 3.23)

pathways visualization annotation multiplecomparison genesetenrichment reactome enrichment-analysis reactome-pathway-analysis reactomepa

13.14 score 46 stars 12 packages 2.5k scripts 9.7k downloads 171 mentions 15 exports 125 dependencies

Last updated from:e295d30981. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	276
linux-devel	OK	515
source / vignettes	OK	332
linux-release	OK	473
macos-release	OK	300
macos-oldrel	OK	345
windows-devel	OK	311
windows-release	OK	404
windows-oldrel	OK	393
wasm-release	OK	248

Exports:bayes_reactome cnetplot dotplot emapplot enrichPathway geneID geneInCategory gseaplot gsePathway gson_Reactome heatplot nsePathway prepareReactomeNetwork ridgeplot viewPathway

Dependencies:AnnotationDbi ape aplot askpass base64enc Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob bslib cachem cli cluster cpp11 crayon curl DBI digest dir.expiry DOSE dplyr enrichit enrichplot evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme openssl patchwork pillar pkgconfig plyr png polyclip purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db reshape2 rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo stringi stringr sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridis viridisLite withr xfun XVector yaml yulab.utils

An R package for Reactome Pathway Analysis

Rendered fromReactomePA.Rmdusingknitr::rmarkdown

Last update: 2026-07-09
Started: 2015-06-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bayesian term selection for Reactome enrichment results	bayes_reactome
Datasets sample contains a sample of gene IDs.	DataSet
Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.	enrichPathway
getDb	getDb
gsePathway	gsePathway
gson_Reactome	gson_Reactome
Network-based Reactome pathway enrichment analysis	nsePathway
Prepare Reactome reaction network for NSEA	prepareReactomeNetwork
viewPathway	viewPathway