Fisher's Test for Enrichment and Depletion of User-Defined Pathways

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Documentation for package ‘fedup’ version 1.13.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

geneDouble	Example list of a background set and two sets of test genes to use for enrichment analysis.
geneMulti	Example list of a background set and multiple sets of test genes to use for enrichment analysis.
geneSingle	Example list of a background set and single set of test genes to use for enrichment analysis.
pathwaysGMT	Named list of human pathway annotations obtained from a GMT file.
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 ggplot.
plotFemap	Draws a network representation of overlaps among pathway enrichment results using EnrichmentMap (EM) in Cytoscape.
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 Fisher's exact test.
writeFemap	Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.
writePathways	Writes a set of pathways (list of vectors) to a GMT file.