DOSE

DOI: 10.18129/B9.bioc.DOSE    

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.7)

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 [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]

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("http://bioc.ism.ac.jp/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 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 3.6.1
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim(>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils
LinkingTo
Suggests BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/software/DOSE
BugReports https://github.com/GuangchuangYu/DOSE/issues
Depends On Me
Imports Me bioCancer, clusterProfiler, debrowser, eegc, enrichplot, facopy, GDCRNATools, LINC, meshes, miRsponge, MoonlightR, PathwaySplice, ReactomePA
Suggests Me GOSemSim
Links To Me
Build Report  

Package Archives

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

Source Package DOSE_3.6.1.tar.gz
Windows Binary DOSE_3.6.1.zip
Mac OS X 10.11 (El Capitan) DOSE_3.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DOSE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DOSE
Package Short Url http://bioconductor.org/packages/DOSE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

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