Man pages for sansomlab/gsfisher
Geneset Fisher
| analyseGenesets | Wrapped to run gene set enrichement on multiple annotation... |
| clusterGenesetsByGenes | Cluster a set of genesets by gene membership |
| ensembl2entrez | Translate ensembl gene ids to entrez gene ids |
| fetchAnnotation | Fetch ENSEMBL ids, ENTREZ ids and gene names using bioMart |
| fetchKEGG | Fetch KEGG pathway annotations |
| filterGenesets | Filter a genesets results table |
| fisherTest | Perform a single Fisher test for gene set enrichement |
| formatDescriptions | Utility function to clean up desriptions for plots |
| getENSEMBL | Get the org.Xx.eg.db ENSEMBL bimap object |
| getEntrez | Verify input gene id type and return entrez identifiers |
| getGO | Get the org.Xx.eg.db GO2ALLEGS bimap object. |
| getSampleGenesets | Get a list of top-genesets by cluster |
| mapENTREZhuman2mouse | Translate ENTREZ gene sets from human to mouse |
| minus_log10_trans | Make a -log10 transform for ggplot. |
| readGMT | Read gene sets from a GMT file |
| runFisherTests | Run a set of Fisher tests for gene set enrichement |
| runGMT | Run gene set enrichement on custom gene sets |
| runGMT.all | Run GMT analysis on a multi-sample results table. |
| runGO | Run gene set enrichement on Gene Ontology categories |
| runGO.all | Run GO analysis on a multi-sample results table. |
| runKEGG | Run gene set enrichement on KEGG pathways |
| runKEGG.all | Run KEGG analysis on a multi-sample results table. |
| sampleEnrichmentDotplot | Make a dot-plot of geneset enrichments across multiple... |
| sampleEnrichmentHeatmap | Draw a heatmap of enriched genesets in all samples |
| visualiseClusteredGenesets | Visulalise a set of clustered genesets on a circular... |
| writeGMT | Write gene sets to a GMT file |
