fgsea

DOI: 10.18129/B9.bioc.fgsea    

Fast Gene Set Enrichment Analysis

Bioconductor version: Release (3.8)

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 [ctb], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

Citation (from within R, enter citation("fgsea")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("fgsea", version = "3.8")

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 Using fgsea package
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.8.0
In Bioconductor since BioC 3.4 (R-3.3) (2 years)
License MIT + file LICENCE
Depends R (>= 3.3), Rcpp
Imports data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery
SystemRequirements C++11
Enhances
URL https://github.com/ctlab/fgsea/
BugReports https://github.com/ctlab/fgsea/issues
Depends On Me gsean, PPInfer
Imports Me CEMiTool, cTRAP, DOSE, mCSEA, phantasus, piano
Suggests Me mdp, Pi
Links To Me
Build Report  

Package Archives

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

Source Package fgsea_1.8.0.tar.gz
Windows Binary fgsea_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) fgsea_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fgsea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fgsea
Package Short Url http://bioconductor.org/packages/fgsea/
Package Downloads Report Download Stats

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