fgsea

Fast Gene Set Enrichment Analysis


Bioconductor version: Release (3.19)

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Author: Gennady Korotkevich [aut], Vladimir Sukhov [aut], Nikolay Budin [ctb], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("fgsea")

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("fgsea")
Gene set co-regulation analysis tutorial HTML R Script
Using fgsea package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (8 years)
License MIT + file LICENCE
Depends R (>= 4.1)
Imports Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils
System Requirements C++11
URL https://github.com/ctlab/fgsea/
Bug Reports https://github.com/ctlab/fgsea/issues
See More
Suggests testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat
Linking To Rcpp, BH
Enhances
Depends On Me gsean, metapone, PPInfer
Imports Me ATACCoGAPS, BioNAR, CelliD, CEMiTool, clustifyr, CoGAPS, cTRAP, DOSE, EventPointer, fobitools, lipidr, mCSEA, MIRit, multiGSEA, NanoTube, nipalsMCIA, omicsViewer, pairedGSEA, phantasus, piano, projectR, RegEnrich, RegionalST, signatureSearch, ViSEAGO, cinaR, DTSEA, mulea, scITD
Suggests Me Cepo, decoupleR, gatom, gCrisprTools, iSEEpathways, mdp, pareg, sparrow, SpliceWiz, ttgsea, easybio, genekitr, GeneNMF, goat, grandR, RCPA, rliger
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package fgsea_1.30.0.tar.gz
Windows Binary fgsea_1.30.0.zip
macOS Binary (x86_64) fgsea_1.30.0.tgz
macOS Binary (arm64) fgsea_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fgsea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fgsea
Bioc Package Browser https://code.bioconductor.org/browse/fgsea/
Package Short Url https://bioconductor.org/packages/fgsea/
Package Downloads Report Download Stats