| 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 |