Scrna Cellstate Annotation

Community

sagirimo

scrna-cellstate-annotation

Assign evidence-backed broad immune cell classes and T-cell states to clustered AnnData data without using clinical outcome labels.

Overview

Publisher	sagirimo
Repository	`BioDSH`
Skill name	`scrna-cellstate-annotation`
Stars	65
Forks	2
Bundled files	3
License	MIT
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.
3 bundled files
Scripts, templates, and references the model can read while it works. Files are read-only and never executed.
Open source
Published by sagirimo on GitHub. Read the source before you install it.

Installation

Install the Scrna Cellstate Annotation 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/sagirimo/BioDSH/tree/main/biodsh-core/skills/scrna-cellstate-annotation
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/sagirimo/BioDSH/tree/main/biodsh-core/skills/scrna-cellstate-annotation

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/sagirimo/BioDSH.git /tmp/BioDSH
mkdir -p .claude/skills
cp -r /tmp/BioDSH/biodsh-core/skills/scrna-cellstate-annotation .claude/skills/scrna-cellstate-annotation

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

Use it in TypingMind

Enable Scrna Cellstate Annotation 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 Scrna Cellstate Annotation 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 Scrna Cellstate Annotation 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.

scRNA-seq cell-state annotation

Use this skill on a normalized AnnData .h5ad input that already contains obs["leiden"] clusters.

Scientific contract

Treat the source file as read-only and verify its SHA-256 before and after execution.
Use expression, gene identifiers, and Leiden clusters only. Never use response, therapy, timepoint, patient, survival, or other clinical outcome metadata to assign labels.
Resolve duplicate gene symbols by selecting the feature with the highest mean expression and report that decision.
Score fixed broad immune and T-cell-state marker programs after per-gene standardization across cells.
Assign labels at cluster level only when at least two program markers are present, the top score is non-negative, and its margin over the runner-up reaches the declared threshold.
Emit unknown when evidence is insufficient. Do not turn marker-program labels into reference truth, clinical diagnosis, or treatment-response claims.
Apply T-cell-state labels only to clusters assigned as T_cell; use not_applicable for other broad classes.

Outputs

annotated.h5ad: input data plus cluster-level broad and T-cell-state annotations.
cell_annotations.csv: cell ID, Leiden cluster, broad class, and T-cell state only; clinical fields are excluded.
cluster_annotation_evidence.csv: cluster size, every program score, selected labels, runner-up labels, and margins.
annotation_report.json: marker coverage, duplicate resolution, thresholds, label counts, leakage guard, versions, and claim boundary.

Bundled files

The model reads these on demand while the skill is loaded. They are exposed as readable files and are never executed.

Frequently asked questions

What does the Scrna Cellstate Annotation AI skill do?

Assign evidence-backed broad immune cell classes and T-cell states to clustered AnnData data without using clinical outcome labels.

Why use Scrna Cellstate Annotation on TypingMind?

Because you install it once and use it with any model. Scrna Cellstate Annotation 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 Scrna Cellstate Annotation in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/sagirimo/BioDSH/tree/main/biodsh-core/skills/scrna-cellstate-annotation. TypingMind reads its SKILL.md and bundles its files and installs it as a skill you can enable per chat.

Which AI models can use Scrna Cellstate Annotation?

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 Scrna Cellstate Annotation?

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

Is the Scrna Cellstate Annotation AI skill free?

Yes. It is published on GitHub by sagirimo under the MIT license. 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

scRNA-seq cell-state annotation

Scientific contract

Outputs

Bundled files

Frequently asked questions

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