Man pages for RCPA
Consensus Pathway Analysis
| downloadGEO | Download GEO data |
| getCePaPathwayCatalogue | Get KEGG pathway catalogue (network) for CePa.ORA and... |
| getCommonDEGenes | Get common significant DE genes from multiple DE Analysis... |
| getCommonPathways | Retrieve common significant pathways from multiple pathway... |
| 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... |
| plotForest | Plot pathway forest plot from pathway/geneset/meta analysis... |
| 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... |
| 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 |
