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RCPA (version 0.2.9)

Consensus Pathway Analysis

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) , Love et al. (2014) , Robinson et al. (2010) , Korotkevich et al. (2016) , Efron et al. (2015) , and Gu et al. (2012) .

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Version

Install

install.packages('RCPA')

Monthly Downloads

312

Version

0.2.9

License

GPL-3

Maintainer

Ha Nguyen

Last Published

July 13th, 2026

Functions in RCPA (0.2.9)

plotForest

Plot pathway forest plot from pathway/geneset/meta analysis results
runPathwayAnalysis

Topology-based Pathway Analysis
runConsensusAnalysis

Perform Consensus Analysis
runDEAnalysis

Differential expression analysis
processAgilent

Process and normalize agilent-based dataset
processAffymetrix

Process and normalize affymetrix-based dataset
runPathwayMetaAnalysis

Perform Meta Analysis
runGeneSetAnalysis

Gene Set Enrichment Analysis
runDEMetaAnalysis

Combine DE analysis results
plotBarChart

Plot a bar chart of the pathway analysis results
getSPIAKEGGNetwork

Get KEGG pathway network for SPIA method
downloadGEO

Download GEO data
getGeneSets

Get gene sets
getSupportedPlatforms

Get supported platforms
getCePaPathwayCatalogue

Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methods
loadData

Load data from GitHub
getCommonDEGenes

Get common significant DE genes from multiple DE Analysis results
getCommonPathways

Retrieve common significant pathways from multiple pathway analysis results
getEntrezAnnotation

Get Entrez annotation
plotDEGeneHeatmap

Plot gene heatmap from a SummarizedExperiment object with DE analysis results
plotVennDE

Plot Venn diagram from multiple DE Analysis results
plotVolcanoDE

Plot volcano plot from Pathway analysis results
plotPathwayNetwork

Plot a pathway network
plotPathwayHeatmap

Plot pathways heatmap plot from pathway/geneset/meta analysis results
plotVolcanoPathway

Plot volcano plot from Pathway analysis results
plotKEGGMap

Plot KEGG map with DE genes
plotVennPathway

Plot Venn diagram from multiple pathway analysis results
plotMA

Plot MA plot from DE analysis results