To install this package, start R and enter:

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

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

DOSE

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: 3.2

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 <guangchuangyu at gmail.com> with contributions from Li-Gen Wang, Vladislav Petyuk and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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")
HTML Disease Ontology Semantic and Enrichment analysis
PDF Reference Manual
Text NEWS

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 2.8.3
In Bioconductor since BioC 2.9 (R-2.14) (4.5 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_2.8.3.tar.gz
Windows Binary DOSE_2.8.3.zip
Mac OS X 10.6 (Snow Leopard) DOSE_2.8.1.tgz
Mac OS X 10.9 (Mavericks) DOSE_2.8.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DOSE/tree/release-3.2
Package Short Url http://bioconductor.org/packages/DOSE/
Package Downloads Report Download Stats

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