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 |