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 (3.0)

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 DOSE - an R package for Disease Ontology Semantic and Enrichment
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 2.4.0
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 3.0.0)
Imports methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, igraph, scales, reshape2, graphics, GOSemSim, grid, ggplot2
Suggests org.Hs.eg.db, clusterProfiler, ReactomePA, ChIPseeker, knitr
System Requirements
URL https://github.com/GuangchuangYu/DOSE
Depends On Me
Imports Me clusterProfiler, facopy, ReactomePA
Suggests Me ChIPseeker, GOSemSim

Package Archives

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

Package Source DOSE_2.4.0.tar.gz
Windows Binary DOSE_2.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DOSE_2.4.0.tgz
Mac OS X 10.9 (Mavericks) DOSE_2.4.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center