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

 

   

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.4)

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

HTML R Script 00 DOSE introduction
HTML R Script 01 DOSE semantic similarity analysis
HTML R Script 02 Disease enrichment analysis
HTML R Script 03 Disease GSEA
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.0.9
In Bioconductor since BioC 2.9 (R-2.14) (5 years)
License Artistic-2.0
Depends R (>= 3.3.1)
Imports AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim(>= 2.0.0), graphics, grDevices, grid, igraph, methods, qvalue, reshape2, S4Vectors, scales, stats, stats4, utils
LinkingTo
Suggests BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat, UpSetR
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/DOSE
BugReports https://github.com/GuangchuangYu/DOSE/issues
Depends On Me clusterProfiler, meshes, ReactomePA
Imports Me bioCancer, ChIPseeker, debrowser, eegc, facopy, LINC, MoonlightR
Suggests Me GOSemSim
Build Report  

Package Archives

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

Package Source DOSE_3.0.9.tar.gz
Windows Binary DOSE_3.0.9.zip
Mac OS X 10.9 (Mavericks) DOSE_3.0.9.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DOSE/tree/release-3.4
Package Short Url http://bioconductor.org/packages/DOSE/
Package Downloads Report Download Stats

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