RCPA: Consensus Pathway Analysis

Provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results (Nguyen et al. (2024) <doi:10.1002/cpz1.1036>). The package is a wrapper of the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.

Version: 0.2.3
Depends: R (≥ 4.0), tidyr, dplyr, ggplot2, utils, stats
Imports: AnnotationDbi, SummarizedExperiment, BiocManager, Biobase, DESeq2, GEOquery, edgeR, limma, stringr (≥ 1.5.0), ggnewscale, ggrepel, graph, httr, rlang, ggpattern, scales, RobustRankAggreg, methods, jsonlite, IRdisplay
Suggests: knitr, rmarkdown, markdown, testthat (≥ 3.0.0), ROntoTools, fgsea, GSA, CePa, meta, png, ggvenn, RCurl, XML, S4Vectors, hgu133plus2.db, org.Hs.eg.db, oligo
Published: 2024-07-03
DOI: 10.32614/CRAN.package.RCPA
Author: Ha Nguyen [aut, cre], Phi Bya [aut], Zeynab Maghsoudi [aut], Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006 at auburn.edu>
BugReports: https://github.com/tinnlab/RCPA/issues
License: GPL-3
NeedsCompilation: no
CRAN checks: RCPA results


Reference manual: RCPA.pdf
Vignettes: RCPA


Package source: RCPA_0.2.3.tar.gz
Windows binaries: r-devel: RCPA_0.2.3.zip, r-release: RCPA_0.2.3.zip, r-oldrel: RCPA_0.2.3.zip
macOS binaries: r-release (arm64): RCPA_0.2.3.tgz, r-oldrel (arm64): RCPA_0.2.3.tgz, r-release (x86_64): RCPA_0.2.3.tgz, r-oldrel (x86_64): RCPA_0.2.3.tgz
Old sources: RCPA archive


Please use the canonical form https://CRAN.R-project.org/package=RCPA to link to this page.