fgsea
Fast Gene Set Enrichment Analysis
Bioconductor version: Release (3.20)
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("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 | 1.32.0 |
| 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 | PPInfer, gsean, metapone |
| Imports Me | BioNAR, CEMiTool, CelliD, CoGAPS, DOSE, DeepTarget, EventPointer, MIRit, MPAC, NanoTube, POMA, RegEnrich, cTRAP, clustifyr, fobitools, lipidr, multiGSEA, nipalsMCIA, omicsViewer, pairedGSEA, pathlinkR, phantasus, piano, projectR, signatureSearch, cinaR, DTSEA, mulea, scITD |
| Suggests Me | Cepo, SpliceWiz, decoupleR, gCrisprTools, gatom, iSEEpathways, mdp, sparrow, ttgsea, easybio, genekitr, GeneNMF, goat, grandR, Platypus, rliger |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fgsea_1.32.0.tar.gz |
| Windows Binary (x86_64) | fgsea_1.32.0.zip |
| macOS Binary (x86_64) | fgsea_1.32.0.tgz |
| macOS Binary (arm64) | fgsea_1.31.6.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 |