Man pages for rosscm/FEDUP
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
| geneDouble | Example list of a background set and two sets of test genes... |
| geneMulti | Example list of a background set and multiple sets of test... |
| geneSingle | Example list of a background set and single set of test genes... |
| pathwaysGMT | Named list of human pathway annotations obtained from a GMT... |
| pathwaysTXT | Example list of SAFE terms obtained from a TXT file. |
| pathwaysXLSX | Example list of SAFE terms obtained from a XLSX file. |
| plotDotPlot | Visualizes fedup enrichment and depletion results using... |
| plotFemap | Draws a network representation of overlaps among pathway... |
| prepInput | Prepares input gene list for runFedup. |
| readPathways | Returns a list of pathways from various file formats. |
| runFedup | Runs pathway enrichment and depletion analysis using a... |
| writeFemap | Writes an enrichment dataset file for use in Cytoscape... |
| writePathways | Writes a set of pathways (list of vectors) to a GMT file. |
