fgsea

DOI:10.18129/B9.bioc.fgsea

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, seefgsea.

Fast Gene Set Enrichment Analysis

Bioconductor version: 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

Installation

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

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age 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) (2.5 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,cTRAP,DOSE,mCSEA,phantasus,piano
Suggests Me	mdp,Pi
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 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	//www.andersvercelli.com/packages/fgsea/
Package Downloads Report	Download Stats