How do I install the Bioconductor Dose skill?

Run npx skillmds@latest add biomate-ai/bioconductor-dose in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bioconductor Dose safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Bioconductor Dose?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bioconductor Dose free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bioconductor Dose?

biomate-ai (@biomate-ai) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bioconductor Dose by biomate-ai — Agent Skill

Name: Bioconductor Dose
Author: biomate-ai

Bioconductor Dose

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

biomate-ai 700e4f0 2.3 KB Updated Sep 17, 2026

File contents

DOSE

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

Version: 4.6.0 · Bioconductor: 3.23 · R: ≥ 4.6
Imports: AnnotationDbi, enrichit, ggplot2, GOSemSim, reshape2, yulab.utils
Install: BiocManager::install("DOSE")

When to Use

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.

References

Homepage: https://bioconductor.org/packages/DOSE
Vignette: https://bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/DOSE.html

Run this on BioMate

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.

▶ Open dose on BioMate →

---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 enric---# DOSE## Dependencies & Environment> Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.- **Version:** 4.6.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6- **Imports:** AnnotationDbi, enrichit, ggplot2, GOSemSim, reshape2, yulab.utils- **Install:** `BiocManager::install("DOSE")`## When to Use- **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.## References- Homepage: https://bioconductor.org/packages/DOSE- Vignette: https://bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/DOSE.html---## Run this on BioMateThis 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](https://www.biomate.ai?ref=kb&pkg=dose)** — free to start.▶ **[Open `dose` on BioMate →](https://www.biomate.ai?ref=kb&pkg=dose)**

Frequently asked questions