DOI: 10.18129/B9.bioc.fedup  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see fedup.

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

Bioconductor version: 3.17

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 mail.utoronto.ca>

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


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


biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats
Suggests biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
URL https://github.com/rosscm/fedup
BugReports https://github.com/rosscm/fedup/issues
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Follow Installation instructions to use this package in your R session.

Source Package fedup_1.8.0.tar.gz
Windows Binary fedup_1.8.0.zip
macOS Binary (x86_64) fedup_1.8.0.tgz
macOS Binary (arm64) fedup_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fedup
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fedup
Bioc Package Browser https://code.bioconductor.org/browse/fedup/
Package Short Url https://bioconductor.org/packages/fedup/
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