fgsea

Fast Gene Set Enrichment Analysis

Bioconductor version: 3.23 · Package version: 1.38.0

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.

Installation

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

BiocManager::install("fgsea")

Details

Maintainer	Alexey Sergushichev <alsergbox@gmail.com>
Author	Gennady Korotkevich [aut], Vladimir Sukhov [aut], Nikita Golikov [aut], Nikolay Budin [ctb], Nikita Gusak [ctb], Zieman Mark [ctb], Alexey Sergushichev [aut, cre]
License	MIT + file LICENCE
URL	https://github.com/alserglab/fgsea/
Bug Reports	https://github.com/alserglab/fgsea/issues
Downloads rank	28101
Source branch	RELEASE_3_23
biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software

Documentation

Download

Source package

Dependencies

Depends: R (>= 4.1)

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

Reverse dependencies

Depends On Me (3): gsean, metapone, PPInfer

Imports Me (36): BioNAR, BioUtils, CelliD, CEMiTool, cinaR, clustifyr, CoGAPS, cTRAP, DeepTarget, DTSEA, EventPointer, fobitools, lipidr, markeR, mCSEA, MIRit, Moonlight2R, MPAC, mulea, multiGSEA, NanoTube, nipalsMCIA, omicsViewer, pairedGSEA, pathlinkR, phantasus, piano, plaid, POMA, postNet, projectR, RegEnrich, RegionalST, scITD, signatureSearch, ViSEAGO

Suggests Me (25): Cepo, craftgrn, decoupleR, easybio, easyLSEA, enrichit, escape, futurize, gatom, gCrisprTools, genekitr, GeneNMF, ggpicrust2, goat, grandR, iSEEpathways, mdp, pathMED, RCPA, rliger, Signac, sparrow, SpliceWiz, TaxSEA, ttgsea