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
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Fast Gene Set Enrichment Analysis
Bioconductor version: Release (3.5)
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Pathways, Software |
| Version | 1.2.1 |
| 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 | DOSE, piano |
| Suggests Me | Pi |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fgsea_1.2.1.tar.gz |
| Windows Binary | fgsea_1.2.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | fgsea_1.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fgsea |
| Package Short Url | http://bioconductor.org/packages/fgsea/ |
| Package Downloads Report | Download Stats |
Documentation »
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