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

Need some help? Ask on the Bioconductor Support site!

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

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	PPInfer, gsean, metapone
Imports Me	ATACCoGAPS, BioNAR, CEMiTool, CelliD, CoGAPS, DOSE, EventPointer, MIRit, NanoTube, RegEnrich, RegionalST, ViSEAGO, cTRAP, clustifyr, fobitools, lipidr, mCSEA, multiGSEA, nipalsMCIA, omicsViewer, pairedGSEA, phantasus, piano, projectR, signatureSearch, cinaR, DTSEA, mulea, scITD
Suggests Me	Cepo, SpliceWiz, decoupleR, gCrisprTools, gatom, iSEEpathways, mdp, pareg, sparrow, ttgsea, easybio, genekitr, GeneNMF, goat, grandR, Platypus, 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 (x86_64)	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