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Bioconductor - fgsea (development version)

fgsea

This is the development version of fgsea; for the stable release version, see fgsea.

Fast Gene Set Enrichment Analysis

Bioconductor version: Development (3.22)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software Version 1.35.6 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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 See More 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, escape, 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.

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