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("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")| 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 | 1.35.8 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 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, markeR, 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.
| Source Package | fgsea_1.35.8.tar.gz |
| Windows Binary (x86_64) | fgsea_1.35.6.zip (64-bit only) |
| macOS Binary (x86_64) | fgsea_1.35.8.tgz |
| macOS Binary (arm64) | fgsea_1.35.8.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 |