To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

fgsea

DOI: 10.18129/B9.bioc.fgsea    

Fast Gene Set Enrichment Analysis

Bioconductor version: Release (3.6)

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: 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

HTML R Script Using fgsea package
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License MIT + file LICENCE
Depends R (>= 3.3), Rcpp
Imports data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel
SystemRequirements C++11
Enhances
URL https://github.com/ctlab/fgsea/
BugReports https://github.com/ctlab/fgsea/issues
Depends On Me PPInfer
Imports Me CEMiTool, DOSE, piano
Suggests Me Pi
Build Report  

Package Archives

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

Source Package fgsea_1.4.0.tar.gz
Windows Binary fgsea_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) fgsea_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fgsea
Package Short Url http://bioconductor.org/packages/fgsea/
Package Downloads Report Download Stats

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