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 3.0 of Bioconductor; for the stable, up-to-date release version, see DOSE.
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: 3.0
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, Li-Gen Wang
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DOSE")
| R Script | DOSE - an R package for Disease Ontology Semantic and Enrichment | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Software, Visualization |
| Version | 2.4.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0) |
| Imports | methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, igraph, scales, reshape2, graphics, GOSemSim, grid, ggplot2 |
| LinkingTo | |
| Suggests | org.Hs.eg.db, clusterProfiler, ReactomePA, ChIPseeker, knitr |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/GuangchuangYu/DOSE |
| Depends On Me | |
| Imports Me | clusterProfiler, facopy, ReactomePA |
| Suggests Me | ChIPseeker, GOSemSim |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DOSE_2.4.0.tar.gz |
| Windows Binary | DOSE_2.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DOSE_2.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | DOSE_2.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DOSE/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/DOSE/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
