To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DOSE")
In most cases, you don't need to download the package archive at all.
DOSE
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: 2.14
Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis.
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:
source("http://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, Software |
| Version | 2.2.1 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), ggplot2 |
| Imports | methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, igraph, scales, reshape2, graphics, GOSemSim, grid |
| Suggests | clusterProfiler, ReactomePA, knitr, org.Hs.eg.db |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | clusterProfiler, ReactomePA |
| Suggests Me | ChIPseeker, GOSemSim |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DOSE_2.2.1.tar.gz |
| Windows Binary | DOSE_2.2.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DOSE_2.2.1.tgz |
| Mac OS X 10.9 (Mavericks) | DOSE_2.2.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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