fedup
This is the development version of fedup; for the stable release version, see fedup.
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
Bioconductor version: Development (3.24)
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("fedup")):Catherine Ross. fedup: Fisher's Test for Enrichment and Depletion of User-Defined Pathways. doi:10.18129/B9.bioc.fedup, R package version 1.21.0, https://bioconductor.org/packages/fedup.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Running fedup with a single test set | HTML |
| Running fedup with multiple test sets | HTML |
| Running fedup with two test sets | HTML |
| Reference Manual |
Details
| biocViews | GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 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 |
See More
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | fedup_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | fedup_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | fedup_1.21.0.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 |