DOSE

This is the development version of DOSE; for the stable release version, see DOSE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Development (3.24)

Provides ontology-aware methods for disease and phenotype knowledge mining. DOSE supports semantic similarity analysis of disease and phenotype ontology terms, genes, and gene clusters using methods including Resnik, Schlicker, Jiang, Lin, and Wang. It also provides over-representation analysis and gene set enrichment analysis for interpreting gene vectors and ranked gene lists in disease, phenotype, and cancer contexts.

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")):

Guangchuang Yu. DOSE: Disease Ontology Semantic and Enrichment analysis. doi:10.18129/B9.bioc.DOSE, R package version 4.7.3, https://bioconductor.org/packages/DOSE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	HTML
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version	4.7.3
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	AnnotationDbi, enrichit (>= 0.2.2), ggplot2, GOSemSim (>= 2.39.2), gson (>= 0.0.5), memoise, methods, reshape2, utils, yulab.utils (> 0.2.2)
System Requirements
URL	https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/GuangchuangYu/DOSE/issues

Suggests	aisdk, clusterProfiler, knitr, org.Hs.eg.db, org.Mm.eg.db, quarto, testthat
Linking To
Enhances
Depends On Me
Imports Me	bioCancer, enrichplot, ExpHunterSuite, GDCRNATools, GOaGO, goatea, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, RegEnrich, scTensor, signatureSearch, SVMDO, TraianProt, vsclust
Suggests Me	BenchHub, clusterProfiler, cola, debrowser, enrichit, ggpicrust2, GOSemSim, GRaNIE, IOBR, rrvgo, scFeatures, scGPS, scGraphVerse, TDbasedUFEadv, wikiprofiler
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DOSE_4.7.3.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	DOSE_4.7.3.tgz
macOS Binary (sonoma-arm64)	DOSE_4.7.0.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	https://bioconductor.org/packages/DOSE/
Package Downloads Report	Download Stats