Disease Ontology Semantic and Enrichment analysis

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.

For enrichment analysis, a discussion forum can be found at https://groups.google.com/forum/#!forum/clusterprofiler.

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://guangchuangyu.github.io

Citation

Please cite the following article when using DOSE:

Yu G, Wang L, Yan G and He Q.
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis.
Bioinformatics, 2015, 31(4):608-609.

URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu684

License

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

Installation

To install:

• the latest released version: biocLite("DOSE")
• the latest development version: devtools::install_github("GuangchuangYu/DOSE")

Documentation

To view the vignette of DOSE installed in your system, start R and enter:

vignette("DOSE", package="DOSE")

More documents can be found in http://www.bioconductor.org/packages/GOSemSim, http://www.bioconductor.org/packages/clusterProfiler and http://guangchuangyu.github.io/tags/dose.

Bugs/Feature requests

• If you have any, let me know. Thx!