Registration Open for Bioc2024 July 24-26


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

Bioconductor version: Release (3.19)

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

Author: Catherine Ross [aut, cre]

Maintainer: Catherine Ross <catherinem.ross at>

Citation (from within R, enter citation("fedup")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

fedup_doubleTest.html HTML R Script
fedup_mutliTest.html HTML R Script
fedup_singleTest.html HTML R Script
Reference Manual PDF


biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats
System Requirements
Bug Reports
See More
Suggests biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package fedup_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) fedup_1.12.0.tgz
macOS Binary (arm64) fedup_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats