fedup

DOI: 10.18129/B9.bioc.fedup  

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

Bioconductor version: Release (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>

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")

 

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

Details

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
LinkingTo
Suggests	biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
SystemRequirements
Enhances
URL	https://github.com/rosscm/fedup
BugReports	https://github.com/rosscm/fedup/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive