Package: RCPA
Type: Package
Title: Consensus Pathway Analysis
Version: 0.2.9
Authors@R: c(
    person(given = "Ha", family = "Nguyen", email = "hvn0006@wayne.edu", role = c("aut", "cre")),
    person(given = "Phi", family = "Bya", role = c("aut")),
    person(given = "Zeynab", family = "Maghsoudi", role = c("aut")),
    person(given = "Tin", family = "Nguyen", role = c("fnd")))
Description: Provides a set of functions to perform pathway analysis
        and meta-analysis from multiple gene expression datasets, as
        well as visualization of the results. This package wraps
        functionality from 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 et al. (2012)
        <https://CRAN.R-project.org/package=CePa>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0), tidyr, dplyr, ggplot2, utils, stats
biocViews: Biobase, DESeq2, GEOquery, edgeR, limma, RCyjs, fgsea,
        BrowserViz, SummarizedExperiment, AnnotationDbi, ROntoTools
Imports: AnnotationDbi, SummarizedExperiment, BiocManager, Biobase,
        DESeq2, GEOquery, edgeR, limma, stringr(>= 1.5.0), ggnewscale,
        ggrepel, graph, httr, rlang, ggpattern, scales,
        RobustRankAggreg, methods, jsonlite, IRdisplay
RoxygenNote: 7.3.2
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
Config/testthat/edition: 3
Config/testthat/stop-on-test-error: false
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/tinnlab/RCPA/issues
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        libicu-dev libpng-dev libxml2-dev libssl-dev libproj-dev
        libsqlite3-dev libudunits2-dev libx11-dev zlib1g-dev
Repository: https://tinnlab.r-universe.dev
Date/Publication: 2026-07-14 13:13:05 UTC
RemoteUrl: https://github.com/tinnlab/rcpa
RemoteRef: HEAD
RemoteSha: f420349743e1690256165e7cc42a60f8e66fc243
NeedsCompilation: no
Packaged: 2026-10-12 10:04:03 UTC; root
Author: Ha Nguyen [aut, cre],
  Phi Bya [aut],
  Zeynab Maghsoudi [aut],
  Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@wayne.edu>