Package: ReactomePA 1.49.0

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 and several functions for visualization. This package is not affiliated with the Reactome team.

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

ReactomePA_1.49.0.tar.gz
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ReactomePA.pdf |ReactomePA.html✨
ReactomePA/json (API)
NEWS

# 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-1.49.0(bioc 3.20)ReactomePA-1.48.0(bioc 3.19)

bioconductor-package

12 exports 2.53 score 121 dependencies 7 dependents 171 mentions

Last updated 2 months agofrom:6ac0ae2d61

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

Dependencies:AnnotationDbi ape aplot askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools colorspace cowplot cpp11 crayon curl data.table DBI digest DOSE dplyr enrichplot fansi farver fastmap fastmatch fgsea formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable HDO.db httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr plyr png polyclip purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db reshape2 rlang RSQLite S4Vectors scales scatterpie shadowtext snow stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XVector yulab.utils zlibbioc

An R package for Reactome Pathway Analysis

Guangchuang Yu

Rendered fromReactomePA.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-12-02
Started: 2015-06-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
getALLEG	getALLEG
getDb	getDb
gsePathway	gsePathway
gson_Reactome	gson_Reactome
viewPathway	viewPathway