DOSE (original) (raw)

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

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Release (3.21)

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

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

Installation

To install this package, start R (version "4.5") 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")

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 4.2.0
In Bioconductor since BioC 2.9 (R-2.14) (13.5 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

See More

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, meshes, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, ReactomePA, RegEnrich, scTensor, signatureSearch, SVMDO, TDbasedUFEadv, ExpHunterSuite, GseaVis, immcp
Suggests Me cola, GOSemSim, GRaNIE, rrvgo, scGPS, ggpicrust2
Links To Me
Build Report Build Report

Package Archives

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

Source Package DOSE_4.2.0.tar.gz
Windows Binary (x86_64) DOSE_4.2.0.zip
macOS Binary (x86_64) DOSE_4.2.0.tgz
macOS Binary (arm64) DOSE_4.2.0.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