To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DOSE")

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

DOSE

 

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.1)

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

Author: Guangchuang Yu, Li-Gen Wang

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DOSE")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DOSE")

 

PDF R Script Disease Ontology Semantic and Enrichment analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 2.6.5
In Bioconductor since BioC 2.9 (R-2.14) (3.5 years)
License Artistic-2.0
Depends R (>= 3.1.0)
Imports methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, igraph, scales, reshape2, graphics, GOSemSim, grid, ggplot2
LinkingTo
Suggests org.Hs.eg.db, clusterProfiler, knitr, BiocStyle
SystemRequirements
Enhances
URL https://github.com/GuangchuangYu/DOSE
BugReports https://github.com/GuangchuangYu/DOSE/issues
Depends On Me
Imports Me clusterProfiler, facopy, ReactomePA
Suggests Me ChIPseeker, GOSemSim
Build Report  

Package Archives

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

Package Source DOSE_2.6.5.tar.gz
Windows Binary DOSE_2.6.5.zip
Mac OS X 10.6 (Snow Leopard) DOSE_2.6.5.tgz
Mac OS X 10.9 (Mavericks) DOSE_2.6.5.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/DOSE/tree/release-3.1
Package Short Url http://bioconductor.org/packages/DOSE/
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