fgsea

DOI: 10.18129/B9.bioc.fgsea    

This is the development version of fgsea; for the stable release version, see fgsea.

Fast Gene Set Enrichment Analysis

Bioconductor version: Development (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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("fgsea")

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 1.7.1
In Bioconductor since BioC 3.4 (R-3.3) (1.5 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, DOSE, mCSEA, phantasus, piano
Suggests Me mdp, Pi
Build Report  

Package Archives

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

Source Package fgsea_1.7.1.tar.gz
Windows Binary fgsea_1.7.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) fgsea_1.7.1.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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