fgsea
This is the released version of fgsea; for the devel version, see fgsea.
Fast Gene Set Enrichment Analysis
Bioconductor version: Release (3.23)
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], Nikita Golikov [aut], Nikolay Budin [ctb], Nikita Gusak [ctb], Zieman Mark [ctb], Alexey Sergushichev [aut, cre]
Maintainer: Alexey Sergushichev <alsergbox at gmail.com>
citation("fgsea")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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/alserglab/fgsea/ |
| Bug Reports | https://github.com/alserglab/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, EventPointer, fobitools, lipidr, markeR, mCSEA, MIRit, Moonlight2R, MPAC, multiGSEA, NanoTube, nipalsMCIA, omicsViewer, pairedGSEA, pathlinkR, phantasus, piano, plaid, POMA, postNet, projectR, RegEnrich, RegionalST, signatureSearch, ViSEAGO, BioUtils, cinaR, DTSEA, mulea, scITD |
| Suggests Me | Cepo, decoupleR, escape, gatom, gCrisprTools, iSEEpathways, mdp, pathMED, sparrow, SpliceWiz, TaxSEA, ttgsea, craftgrn, easybio, easyLSEA, enrichit, futurize, genekitr, GeneNMF, ggpicrust2, goat, grandR, RCPA, rliger, Signac |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fgsea_1.38.0.tar.gz |
| Windows Binary (x86_64) | fgsea_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | fgsea_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | fgsea_1.38.0.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 |