fgsea

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see fgsea.

Fast Gene Set Enrichment Analysis

Bioconductor version: 3.21

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], Nikita Gusak [ctb], Zieman Mark [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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software

Version 1.34.2

In Bioconductor since BioC 3.4 (R-3.3) (9 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

URL https://github.com/ctlab/fgsea/

Bug Reports https://github.com/ctlab/fgsea/issues

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 BioNAR, CelliD, CEMiTool, clustifyr, CoGAPS, cTRAP, DeepTarget, DOSE, EventPointer, fobitools, lipidr, mCSEA, MIRit, MPAC, multiGSEA, NanoTube, nipalsMCIA, omicsViewer, pairedGSEA, pathlinkR, phantasus, piano, POMA, projectR, RegEnrich, RegionalST, signatureSearch, ViSEAGO, cinaR, DTSEA, mulea, scITD

Suggests Me Cepo, decoupleR, gatom, gCrisprTools, iSEEpathways, mdp, pathMED, sparrow, SpliceWiz, TaxSEA, ttgsea, easybio, genekitr, GeneNMF, ggpicrust2, goat, grandR, Platypus, 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_1.34.2.tar.gz

Windows Binary (x86_64) fgsea_1.34.2.zip

macOS Binary (x86_64) fgsea_1.34.2.tgz

macOS Binary (arm64) fgsea_1.34.2.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

Old Source Packages for BioC 3.21 Source Archive