fedup

This package is for version 3.21 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: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

Suggests biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr

Linking To

Enhances

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_1.16.0.tar.gz

Windows Binary (x86_64) fedup_1.16.0.zip

macOS Binary (x86_64) fedup_1.16.0.tgz

macOS Binary (arm64) fedup_1.16.0.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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