Package: RCPA
Type: Package
Title: Consensus Pathway Analysis
Version: 0.2.8
Authors@R: c(
    person(given = "Ha", family = "Nguyen", email = "hvn0006@auburn.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
NeedsCompilation: no
Packaged: 2025-09-15 13:48:48 UTC; hanguyen
Author: Ha Nguyen [aut, cre],
  Phi Bya [aut],
  Zeynab Maghsoudi [aut],
  Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@auburn.edu>
Repository: CRAN
Date/Publication: 2025-09-15 14:10:02 UTC
Built: R 4.6.0; ; 2025-11-13 04:49:48 UTC; windows
