# Consensus Pathway Analysis

## Documentation for package ‘RCPA’ version 0.2.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

downloadGEO | Download GEO data
getCePaPathwayCatalogue | Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methods
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
getGeneSets | Get gene sets
getSPIAKEGGNetwork | Get KEGG pathway network for SPIA method
getSupportedPlatforms | Get supported platforms
loadData | Load data from GitHub
plotBarChart | Plot a bar chart of the pathway analysis results
plotDEGeneHeatmap | Plot gene heatmap from a SummarizedExperiment object with DE analysis results
plotForest | Plot pathway forest plot from pathway/geneset/meta analysis results
plotKEGGMap | Plot KEGG map with DE genes
plotMA | Plot MA plot from DE analysis results
plotPathwayHeatmap | Plot pathways heatmap plot from pathway/geneset/meta analysis results
plotPathwayNetwork | Plot a pathway network
plotVennDE | Plot Venn diagram from multiple DE Analysis results
plotVennPathway | Plot Venn diagram from multiple pathway analysis results
plotVolcanoDE | Plot volcano plot from Pathway analysis results
plotVolcanoPathway | Plot volcano plot from Pathway analysis results
processAffymetrix | Process and normalize affymetrix-based dataset
processAgilent | Process and normalize agilent-based dataset
runConsensusAnalysis | Perform Consensus Analysis
runDEAnalysis | Differential expression analysis
runDEMetaAnalysis | Combine DE analysis results
runGeneSetAnalysis | Gene Set Enrichment Analysis
runPathwayAnalysis | Topology-based Pathway Analysis
runPathwayMetaAnalysis | Perform Meta Analysis