DOSE: 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.

DOSE is released within the Bioconductor project and the source code is hosted in GitHub.

Author

Guangchuang Yu, School of Basic Medical Sciences, Southern Medical University.

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Citation

Please cite the following article when using DOSE:

citation

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

Installation

Install DOSE is easy, follow the guide in the Bioconductor page:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("DOSE")

Overview

Semantic similarity measurement

  • DO term semantic similarity
  • Gene semantic similarity

Enrichment Analysis

  • DO (Disease Ontology)
  • NCG (Network of Cancer Genes)
  • DisGeNet (gene-disease and SNP-disease associations)

Visualization

  • barplot
  • cnetplot
  • dotplot
  • enrichMap
  • gseaplot
  • simplot
  • upsetplot

Find out details and examples on Documentation.

Projects that depend on DOSE

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