fedup

DOI: 10.18129/B9.bioc.fedup    

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

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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_1.2.0.tar.gz
Windows Binary fedup_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) fedup_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fedup
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fedup
Package Short Url https://bioconductor.org/packages/fedup/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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