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DOSE

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.17)

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], Erqiang Hu [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
DOSE HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.26.1
In Bioconductor since BioC 2.9 (R-2.14) (12 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim(>= 2.23.1), methods, qvalue, reshape2, stats, utils
Linking To
Suggests prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, testthat
System Requirements
Enhances
URL https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports https://github.com/GuangchuangYu/DOSE/issues
See More
Depends On Me
Imports Me bioCancer, clusterProfiler, debrowser, eegc, enrichplot, ExpHunterSuite, GDCRNATools, MAGeCKFlute, meshes, miRspongeR, MoonlightR, pareg, Pigengene, ReactomePA, RegEnrich, scTensor, signatureSearch, SVMDO, TDbasedUFEadv
Suggests Me cola, GOSemSim, GRaNIE, rrvgo, scGPS, simplifyEnrichment
Links To Me
Build Report  

Package Archives

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

Source Package DOSE_3.26.1.tar.gz
Windows Binary DOSE_3.26.1.zip
macOS Binary (x86_64) DOSE_3.26.1.tgz
macOS Binary (arm64) DOSE_3.26.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DOSE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DOSE
Bioc Package Browser https://code.bioconductor.org/browse/DOSE/
Package Short Url https://bioconductor.org/packages/DOSE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive