RCPA

CRANRCPAMaRDI QIDQ159073

Consensus Pathway Analysis

Phi Hung Bya, Zeynab Maghsoudi, Ha Nguyen

Last update: 30 November 2023

Copyright license: GNU General Public License, version 3.0

Software version identifier: 0.1.0, 0.1.1, 0.1.2, 0.2.1

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. 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>.

Cites work

• Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
• limma powers differential expression analyses for RNA-sequencing and microarray studies
• edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

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