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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, Bioplanet 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>

Citation (from within R, enter citation("fenr")):

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

Details

biocViews DifferentialExpression, FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Proteomics, Reactome, Software
Version 1.0.5
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, httr2, rvest, progress, biomaRt, BiocFileCache, shiny, ggplot2
System Requirements
URL https://github.com/bartongroup/fenr
Bug Reports https://github.com/bartongroup/fenr/issues
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, topGO
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 fenr_1.0.5.tar.gz
Windows Binary fenr_1.0.5.zip
macOS Binary (x86_64) fenr_1.0.5.tgz
macOS Binary (arm64) fenr_1.0.5.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