DOSE

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis


Bioconductor version: 3.7

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 "3.5") 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")
00 DOSE introduction HTML R Script
01 DOSE semantic similarity analysis HTML R Script
02 Disease enrichment analysis HTML R Script
03 Disease GSEA HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.6.1
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
URL https://guangchuangyu.github.io/software/DOSE
Bug Reports https://github.com/GuangchuangYu/DOSE/issues
See More
Suggests BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat
Linking To
Enhances
Depends On Me
Imports Me bioCancer, clusterProfiler, debrowser, eegc, enrichplot, facopy, GDCRNATools, LINC, MAGeCKFlute, meshes, miRsponge, MoonlightR, PathwaySplice, ReactomePA
Suggests Me GOSemSim
Links To Me
Build Report Build Report

Package Archives

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

Source Package DOSE_3.6.1.tar.gz
Windows Binary DOSE_3.6.1.zip
Mac OS X 10.11 (El Capitan) DOSE_3.6.1.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 3.7 Source Archive