Bioconductor Experimenthub

Organization

bioMate-AI

bioconductor-experimenthub

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me

Overview

Publisher	bioMate-AI
Repository	`biomate-bioconductor-kb`
Skill name	`bioconductor-experimenthub`
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 Experimenthub 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/general/experimenthub
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/general/experimenthub

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/general/experimenthub .claude/skills/bioconductor-experimenthub

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

Use it in TypingMind

Enable Bioconductor Experimenthub 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 Experimenthub 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 Experimenthub 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.

ExperimentHub

Dependencies & Environment

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

Version: 3.2.0 · Bioconductor: 3.23 · R: ≥ 4.6
Depends: BiocGenerics, AnnotationHub, BiocFileCache
Imports: S4Vectors, BiocManager, rappdirs
Install: BiocManager::install("ExperimentHub")

When to Use

Accessing Curated Datasets: Retrieving large files of curated data from experiments, publications, or training courses via the ExperimentHub web service.
Retrieving R Objects: Downloading specific R data objects like SummarizedExperiment, ExpressionSet, or GAlignmentPairs directly into your session.
Interactive Exploration: Interactively querying and exploring available resources using BiocHubsShiny.

When NOT to Use

For accessing reference genome annotations, use AnnotationHub because ExperimentHub is focused exclusively on experimental data.

Data Requirements

Requires an internet connection to download files initially, which are then cached locally.
Queries use string terms (e.g., "mus musculus" or "alpineData").

Key Parameters

localHub: Set to TRUE in ExperimentHub to use only the local cache and avoid internet queries.
ask: Set to FALSE in removeCache to bypass interactive prompts when deleting the cache.
appname: Used in rappdirs::user_cache_dir to specify the package name (e.g., "ExperimentHub").
which: Used in tools::R_user_dir to specify the directory type (e.g., "cache").

Best Practices

Use query to search for specific strings and filter the ExperimentHub object before downloading.
Check snapshotDate and use possibleDates to ensure reproducibility with older versions of a snapshot.
Manage the default caching location using tools::R_user_dir or by setting the EXPERIMENT_HUB_CACHE environment variable.

Common Pitfalls

Proxy Issues: Operating behind a proxy blocks downloads; fix by setting the EXPERIMENT_HUB_PROXY environment variable or using setExperimentHubOption.
Permission Errors: Sharing a cache across multiple users causes access failures; fix by changing the group permissions of BiocFileCache.sqlite and BiocFileCache.sqlite.LOCK to g+rw.
Lost Cache: Upgrading to newer versions changes the default cache location; fix by moving files to the new tools::R_user_dir location or setting EXPERIMENT_HUB_CACHE.

Alternatives

AnnotationHub: For retrieving annotation resources rather than experiment data.
BiocHubsShiny: For a graphical interface to perform the same queries interactively.

Citations

ExperimentHub Package Authors. ExperimentHub: Access the ExperimentHub Web Service. Bioconductor.

References

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

Run this on BioMate

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

▶ Open experimenthub on BioMate →

Frequently asked questions

What does the Bioconductor Experimenthub AI skill do?

Why use Bioconductor Experimenthub on TypingMind?

Because you install it once and use it with any model. Bioconductor Experimenthub 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 Experimenthub in TypingMind?

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

Which AI models can use Bioconductor Experimenthub?

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 Experimenthub?

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

Is the Bioconductor Experimenthub 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

ExperimentHub

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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