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. 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: 0.2.1
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: 2023-11-30
Author: Ha Nguyen [aut, cre], Zeynab Maghsoudi [aut], Phi Hung Bya [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

Documentation:

Reference manual: RCPA.pdf
Vignettes: RCPA

Downloads:

Package source: RCPA_0.2.1.tar.gz
Windows binaries: r-prerel: RCPA_0.2.1.zip, r-release: RCPA_0.2.1.zip, r-oldrel: RCPA_0.2.1.zip
macOS binaries: r-prerel (arm64): RCPA_0.2.1.tgz, r-release (arm64): RCPA_0.2.1.tgz, r-oldrel (arm64): RCPA_0.2.1.tgz, r-prerel (x86_64): RCPA_0.2.1.tgz, r-release (x86_64): RCPA_0.2.1.tgz
Old sources: RCPA archive

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