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
