DOI: 10.18129/B9.bioc.fgsea  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see fgsea.

Fast Gene Set Enrichment Analysis

Bioconductor version: 3.17

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")):


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


biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.26.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License MIT + file LICENCE
Depends R (>= 3.3)
Imports Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils
LinkingTo Rcpp, BH
Suggests testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat
SystemRequirements C++11
URL https://github.com/ctlab/fgsea/
BugReports https://github.com/ctlab/fgsea/issues
Depends On Me gsean, metapone, PPInfer
Imports Me ASpediaFI, ATACCoGAPS, BioNAR, CelliD, CEMiTool, clustifyr, CoGAPS, cTRAP, DOSE, EventPointer, fobitools, lipidr, mCSEA, multiGSEA, NanoTube, omicsViewer, pairedGSEA, phantasus, piano, RegEnrich, signatureSearch, ViSEAGO
Suggests Me Cepo, decoupleR, gCrisprTools, mdp, pareg, Pi, sparrow, SpliceWiz, ttgsea
Links To Me
Build Report  

Package Archives

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Source Package fgsea_1.26.0.tar.gz
Windows Binary fgsea_1.26.0.zip
macOS Binary (x86_64) fgsea_1.26.0.tgz
macOS Binary (arm64) fgsea_1.26.0.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/
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