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. 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>.

Version:	0.2.5
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, pd.hg.u133.plus.2, oligo
Published:	2024-11-06
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
Citation:	RCPA citation info
CRAN checks:	RCPA results

Documentation:

Reference manual:	RCPA.pdf
Vignettes:	RCPA (source, R code)

Downloads:

Package source:	RCPA_0.2.5.tar.gz
Windows binaries:	r-devel: RCPA_0.2.5.zip, r-release: RCPA_0.2.5.zip, r-oldrel: RCPA_0.2.5.zip
macOS binaries:	r-release (arm64): RCPA_0.2.5.tgz, r-oldrel (arm64): RCPA_0.2.5.tgz, r-release (x86_64): RCPA_0.2.5.tgz, r-oldrel (x86_64): RCPA_0.2.5.tgz
Old sources:	RCPA archive

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