fgsea

DOI: 10.18129/B9.bioc.fgsea  

Fast Gene Set Enrichment Analysis

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	geseca-tutorial
HTML	R Script	Using fgsea package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	MIT + file LICENCE
Depends	R (>= 3.3)
Imports	Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, utils
LinkingTo	Rcpp, BH
Suggests	testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation
SystemRequirements	C++11
Enhances
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, cTRAP, DOSE, EventPointer, fobitools, lipidr, mCSEA, multiGSEA, NanoTube, omicsViewer, phantasus, piano, RegEnrich, signatureSearch, ViSEAGO
Suggests Me	Cepo, decoupleR, gCrisprTools, mdp, pareg, Pi, sparrow, ttgsea
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	fgsea_1.24.0.tar.gz
Windows Binary	fgsea_1.24.0.zip
macOS Binary (x86_64)	fgsea_1.24.0.tgz
macOS Binary (arm64)	fgsea_1.24.0.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