Bioconductor Biocviews

Organization

bioMate-AI

bioconductor-biocviews

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '

Overview

Publisher	bioMate-AI
Repository	`biomate-bioconductor-kb`
Skill name	`bioconductor-biocviews`
Stars	804
Forks	66
Bundled files	Instructions only
Links	Skill source Repository

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by bioMate-AI on GitHub. Read the source before you install it.

Installation

Install the Bioconductor Biocviews AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/genomics/biocviews
Enable the skill in any chat where you want it available.

Store

Installed

Skills

Add skills

Import one or more skills from a public GitHub folder or a local .skill or .zip archive, or SKILL.md file.

From GitHub URLFrom .skill, .zip, or SKILL.md

GitHub repo or folder

https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/genomics/biocviews

Points to a single skill folder, or any folder that contains multiple skills. Public repos only.

CancelContinue

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git /tmp/biomate-bioconductor-kb
mkdir -p .claude/skills
cp -r /tmp/biomate-bioconductor-kb/skills/genomics/biocviews .claude/skills/bioconductor-biocviews

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Bioconductor Biocviews in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Bioconductor Biocviews on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Bioconductor Biocviews is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

biocViews

Dependencies & Environment

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

Version: 1.80.0 · Bioconductor: 3.23 · R: ≥ 4.6
Imports: Biobase, graph, RBGL, XML, RCurl, RUnit, BiocManager
Install: BiocManager::install("biocViews")

When to Use

Generating repository HTML and control files (PACKAGES, VIEWS) for a CRAN-style layout using genReposControlFiles and writeRepositoryHtml.
Extracting package vignettes from source packages to a local directory using extractVignettes.
Querying a repository to generate a list of BiocViews objects for specific top-level terms (e.g., "Software") using getBiocSubViews.
Querying available vocabulary subterms from a graphNEL object using getSubTerms.

When NOT to Use

For general package development tasks like linting or unit testing; use BiocCheck or devtools instead because biocViews focuses on repository HTML and vocabulary generation.
For searching Bioconductor packages interactively in a user-friendly GUI; use the Bioconductor website search or BiocPkgTools instead because biocViews generates static HTML views.

Data Requirements

A CRAN-style repository directory containing source packages (src/contrib) and binary packages (bin/windows/contrib, bin/macosx/contrib).
A vocabulary of terms defined in a dot format file (e.g., biocViewsVocab.dot) which is converted to a graphNEL object.

Key Parameters

reposRoot: The top-level directory path for the repository.
contribPaths: A named character vector specifying paths to source and binary packages.
reposUrl: The URL or file path of the repository to query.
topTerm: The top-level vocabulary node to query (e.g., "Software").
term: The base term for which all subterms should be returned in getSubTerms.
dir: Output directory path for generated HTML views in writeBiocViews.

Best Practices

Establish a standard CRAN-style layout with src/contrib and bin directories before running genReposControlFiles.
Extract vignettes using extractVignettes before generating the repository HTML.
Use getBiocSubViews with a valid graphNEL vocabulary object (like biocViewsVocab) to categorize packages.
Generate the final HTML views using writeBiocViews pointing to a dedicated output directory.

Common Pitfalls

Missing repository structure: Running genReposControlFiles without the correct contribPaths names. Fix: Ensure the contribPaths vector has exact names like "source", "win.binary", and "mac.binary".
Vocabulary terms with spaces: Adding terms to the dot file with spaces, which breaks the graph. Fix: Ensure terms use underscores instead of spaces.
Missing tools for vocabulary update: Failing to convert the dot file to GXL. Fix: Ensure dot2gxl from graphviz is installed and on your PATH.

Alternatives

BiocPkgTools: For advanced, user-facing exploration and network analysis of Bioconductor packages and their metadata.
BiocCheck: For verifying package compliance with Bioconductor standards, including biocViews validation.
pkgdown: For generating documentation websites for individual R packages rather than entire repositories.

Citations

Gentleman, R. et al. (2024). biocViews: Categorized views of R package repositories. R package version 1.74.0.

References

Homepage: bioconductor.org/packages/biocViews
Vignette: https://bioconductor.org/packages/release/bioc/vignettes/biocViews/inst/doc/biocViews-HOWTO.pdf

Run this on BioMate

This skill is the knowledge layer — when, why, and how to use biocviews. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

▶ Open biocviews on BioMate →

Frequently asked questions

What does the Bioconductor Biocviews AI skill do?

Why use Bioconductor Biocviews on TypingMind?

Because you install it once and use it with any model. Bioconductor Biocviews is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Bioconductor Biocviews in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/genomics/biocviews. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Bioconductor Biocviews?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Bioconductor Biocviews?

As many as you like. As long as a model supports skills, you can use Bioconductor Biocviews with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Bioconductor Biocviews AI skill free?

It is published on GitHub by bioMate-AI. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

biocViews

Dependencies & Environment

When to Use

When NOT to Use

Data Requirements

Key Parameters

Best Practices

Common Pitfalls

Alternatives

Citations

References

Run this on BioMate

Frequently asked questions

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