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 enric
Start a fresh conversation. Replace the highlighted placeholders.
Use bioconductor-dose to perform a Disease Ontology enrichment and semantic-similarity analysis for [gene identifiers], using [background gene universe] and [analysis goals], and return interpretable enriched disease terms with the required publication citation.
Required inputs
[gene identifiers]
[background gene universe]
[analysis goals]
User-approved starter prompt based on a pinned source version; check current skill requirements before running. Task evidence ↗
SKILL.md
name: bioconductor-dosedescription: 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 enricwhen_to_use: "Use when: Disease Ontology Analysis: Performing Disease Ontology Semantic and Enrichment analysis as described by the package authors.. Not for: For formatting R markdown documents, use knitr because DOSE is strictly for Disease Ontology analysis."user-invocable: false
DOSE
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
Disease Ontology Analysis: Performing Disease Ontology Semantic and Enrichment analysis as described by the package authors.
When NOT to Use
For formatting R markdown documents, use knitr because DOSE is strictly for Disease Ontology analysis.
Data Requirements
Requires loading the package into the R session via library(DOSE).
Key Parameters
pkg: Used in the Biocpkg function example to format package links.
tidy: Used in knitr::opts_chunk$set to control code formatting.
Best Practices
Load the package using library(DOSE).
Cite the primary publication (Yu et al. 2015) when using DOSE in published research.
Common Pitfalls
Missing Citation: Forgetting to cite the package in publications; fix by including the citation to Bioinformatics 2015.
Alternatives
knitr: For document generation and vignette formatting, as it handles markdown chunk options rather than biological enrichment.
Citations
G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.
This skill is the knowledge layer — when, why, and how to use dose. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.