Package: ReactomePA 1.51.0

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_1.51.0.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-1.51.0(bioc 3.21)ReactomePA-1.50.0(bioc 3.20)

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

12.19 score 37 stars 7 packages 1.0k scripts 4.0k downloads 171 mentions 12 exports 123 dependencies

Last updated 24 days agofrom:e581e3e12f. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

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 ggtangle ggtree glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable 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 R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db reshape2 rlang RSQLite S4Vectors scales scatterpie 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 Oct 31 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