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("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 | ||
NEWS | Text |
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 |
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 | ATACCoGAPS, BioNAR, CelliD, CEMiTool, clustifyr, CoGAPS, cTRAP, DOSE, EventPointer, fobitools, lipidr, mCSEA, MIRit, multiGSEA, NanoTube, nipalsMCIA, omicsViewer, pairedGSEA, phantasus, piano, projectR, RegEnrich, RegionalST, signatureSearch, ViSEAGO, cinaR, DTSEA, mulea, scITD |
Suggests Me | Cepo, decoupleR, gatom, gCrisprTools, iSEEpathways, mdp, pareg, sparrow, SpliceWiz, ttgsea, easybio, genekitr, GeneNMF, goat, grandR, 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_1.30.0.tar.gz |
Windows Binary | 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 |