Bioconductor Microbiome

Organization

bioMate-AI

bioconductor-microbiome

Utilities for microbiome analysis.

Overview

Publisher	bioMate-AI
Repository	`biomate-bioconductor-kb`
Skill name	`bioconductor-microbiome`
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 Microbiome 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/metagenomics/microbiome
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/metagenomics/microbiome

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/metagenomics/microbiome .claude/skills/bioconductor-microbiome

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

Use it in TypingMind

Enable Bioconductor Microbiome 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 Microbiome 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 Microbiome 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.

microbiome

Dependencies & Environment

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

Version: 1.34.0 · Bioconductor: 3.23 · R: ≥ 4.6
Depends: phyloseq, ggplot2
Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, tibble, tidyr, vegan
Install: BiocManager::install("microbiome")

When to Use

Facilitating phyloseq-based exploration and analysis of taxonomic profiling data.
Performing manipulation, statistical analysis, and visualization of taxonomic profiling data.
Standardizing analyses and developing best practices for targeted microbiome analysis.

When NOT to Use

For new projects or multi-omics data analysis, use the miaverse project instead, as microbiome development has been discontinued.
For workflows based on the new TreeSummarizedExperiment data container, use miaverse packages instead of microbiome.

Data Requirements

Taxonomic profiling data in the independent phyloseq data format.

Key Parameters

No parameters are explicitly detailed in the provided vignette text.

Best Practices

Transition to the miaverse project and TreeSummarizedExperiment data container for added capabilities in multi-omics data analysis.
Use the package to facilitate scalable exploration of population cohorts and targeted case-control studies.
Rely on the independent phyloseq package and data structures for R-based microbiome analysis.

Common Pitfalls

Using discontinued software for new multi-omics projects: The microbiome package development is discontinued. Fix: Shift to miaverse tools based on TreeSummarizedExperiment.
Incompatibility with new data containers: Attempting to use TreeSummarizedExperiment objects directly in microbiome. Fix: Use phyloseq format or migrate to miaverse.
Missing general-purpose tools: Relying solely on microbiome for all analyses. Fix: Integrate with the independent phyloseq package and its data structures.

Alternatives

phyloseq: The independent package and data structure for R-based microbiome analysis that microbiome relies heavily upon.
miaverse: The recommended successor project based on the TreeSummarizedExperiment data container.

Citations

Leo Lahti et al. (Bioconductor, 2017-2020). Tools for microbiome analysis in R. Microbiome package version.

References

Homepage: https://bioconductor.org/packages/microbiome
Vignette: https://bioconductor.org/packages/release/bioc/vignettes/microbiome

Run this on BioMate

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

▶ Open microbiome on BioMate →

Frequently asked questions

What does the Bioconductor Microbiome AI skill do?

Utilities for microbiome analysis.

Why use Bioconductor Microbiome on TypingMind?

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

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

Which AI models can use Bioconductor Microbiome?

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 Microbiome?

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

Is the Bioconductor Microbiome 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

microbiome

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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