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