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fedup

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


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fedup")

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

Documentation

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

browseVignettes("fedup")
fedup_doubleTest.html HTML R Script
fedup_mutliTest.html HTML R Script
fedup_singleTest.html HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software
Version 1.10.0
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
URL https://github.com/rosscm/fedup
Bug Reports https://github.com/rosscm/fedup/issues
See More
Suggests biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
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Package Archives

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

Source Package fedup_1.10.0.tar.gz
Windows Binary fedup_1.10.0.zip
macOS Binary (x86_64) fedup_1.10.0.tgz
macOS Binary (arm64) fedup_1.10.0.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/
Package Downloads Report Download Stats