fenr

DOI: 10.18129/B9.bioc.fenr  

Fast functional enrichment for interactive applications

Bioconductor version: Release (3.18)

Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

Author: Marek Gierlinski [aut, cre]

Maintainer: Marek Gierlinski <M.Gierlinski at dundee.ac.uk>

Installation

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

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

BiocManager::install("fenr")

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("fenr")

 

HTML	R Script	Fast functional enrichment
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Proteomics, Reactome, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr, XML, jsonlite, progress, biomaRt, BiocFileCache, shiny, ggplot2
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, topGO, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/bartongroup/fenr
BugReports	https://github.com/bartongroup/fenr/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	fenr_1.0.0.tar.gz
Windows Binary	fenr_1.0.0.zip
macOS Binary (x86_64)	fenr_1.0.0.tgz
macOS Binary (arm64)	fenr_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fenr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fenr
Bioc Package Browser	https://code.bioconductor.org/browse/fenr/
Package Short Url	https://bioconductor.org/packages/fenr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive