Learn R Programming
⚠️There's a newer version (0.2.7) of this package.Take me there.

RCPA (version 0.2.6)

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) .

Copy Link

Version

Install

install.packages('RCPA')

Monthly Downloads

481

Version

0.2.6

License

GPL-3

Maintainer

Ha Nguyen

Last Published

April 30th, 2025

Functions in RCPA (0.2.6)

plotPathwayHeatmap

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

Plot a pathway network
plotVennPathway

Plot Venn diagram from multiple pathway analysis results
plotKEGGMap

Plot KEGG map with DE genes
plotMA

Plot MA plot from DE analysis results
plotVennDE

Plot Venn diagram from multiple DE Analysis results
plotForest

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

Combine DE analysis results
runPathwayAnalysis

Topology-based Pathway Analysis
processAgilent

Process and normalize agilent-based dataset
runPathwayMetaAnalysis

Perform Meta Analysis
processAffymetrix

Process and normalize affymetrix-based dataset
runGeneSetAnalysis

Gene Set Enrichment Analysis
runConsensusAnalysis

Perform Consensus Analysis
runDEAnalysis

Differential expression analysis
getSPIAKEGGNetwork

Get KEGG pathway network for SPIA method
plotBarChart

Plot a bar chart of the pathway analysis results
getSupportedPlatforms

Get supported platforms
downloadGEO

Download GEO data
getCePaPathwayCatalogue

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

Get gene sets
loadData

Load data from GitHub
getCommonDEGenes

Get common significant DE genes from multiple DE Analysis results
getEntrezAnnotation

Get Entrez annotation
getCommonPathways

Retrieve common significant pathways from multiple pathway analysis results
plotVolcanoPathway

Plot volcano plot from Pathway analysis results
plotDEGeneHeatmap

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

Plot volcano plot from Pathway analysis results