To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOSE")
In most cases, you don't need to download the package archive at all.
DOSE
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see DOSE.
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: 3.4
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 <guangchuangyu at gmail.com> with contributions from Li-Gen Wang, Vladislav Petyuk and Giovanni Dall'Olio.
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation (from within R,
enter citation("DOSE")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOSE")
Documentation
| HTML | R Script | 00 DOSE introduction |
| HTML | R Script | 01 DOSE semantic similarity analysis |
| HTML | R Script | 02 Disease enrichment analysis |
| HTML | R Script | 03 Disease GSEA |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
| Version | 3.0.10 |
| In Bioconductor since | BioC 2.9 (R-2.14) (5.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.1) |
| Imports | AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim(>= 2.0.0), graphics, grDevices, grid, igraph, methods, qvalue, reshape2, S4Vectors, scales, stats, stats4, utils |
| LinkingTo | |
| Suggests | BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat, UpSetR |
| SystemRequirements | |
| Enhances | |
| URL | https://guangchuangyu.github.io/DOSE |
| BugReports | https://github.com/GuangchuangYu/DOSE/issues |
| Depends On Me | clusterProfiler, meshes, ReactomePA |
| Imports Me | bioCancer, ChIPseeker, debrowser, eegc, facopy, LINC, MoonlightR |
| Suggests Me | GOSemSim |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DOSE_3.0.10.tar.gz |
| Windows Binary | DOSE_3.0.10.zip |
| Mac OS X 10.9 (Mavericks) | DOSE_3.0.10.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DOSE/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/DOSE/ |
| Package Downloads Report | Download Stats |
Documentation »
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