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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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Gene set co-regulation analysis tutorial HTML R Script
Using fgsea package HTML R Script
Reference Manual PDF


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
Bug Reports
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Suggests testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel,, limma, GEOquery, msigdbr, aggregation, Seurat
Linking To Rcpp, BH
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, 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 (64-bit only)
macOS Binary (x86_64) fgsea_1.30.0.tgz
macOS Binary (arm64) fgsea_1.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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