DOSE

DOI: 10.18129/B9.bioc.DOSE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DOSE")

For older versions of R, please refer to the appropriate Bioconductor release.

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	3.8.2
In Bioconductor since	BioC 2.9 (R-2.14) (7.5 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, MAGeCKFlute, meshes, miRsponge, MoonlightR, PathwaySplice, ReactomePA, RNASeqR
Suggests Me	GOSemSim
Links To Me
Build Report

Package Archives

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

Source Package	DOSE_3.8.2.tar.gz
Windows Binary	DOSE_3.8.2.zip
Mac OS X 10.11 (El Capitan)	DOSE_3.8.2.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