DOSE

This is the released version of DOSE; for the devel version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.20)

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 (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version	4.0.0
In Bioconductor since	BioC 2.9 (R-2.14) (13 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim(>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6)
System Requirements
URL	https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/GuangchuangYu/DOSE/issues

Suggests	prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me	bioCancer, clusterProfiler, debrowser, enrichplot, enrichViewNet, GDCRNATools, MAGeCKFlute, meshes, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, ReactomePA, RegEnrich, scTensor, signatureSearch, SVMDO, TDbasedUFEadv, ExpHunterSuite, GseaVis, immcp
Suggests Me	cola, GOSemSim, GRaNIE, rrvgo, scGPS, aPEAR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	DOSE_4.0.0.tar.gz
Windows Binary (x86_64)	DOSE_4.0.0.zip
macOS Binary (x86_64)	DOSE_4.0.0.tgz
macOS Binary (arm64)	DOSE_4.0.0.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