Scrna Inspect Qc

Community

sagirimo

scrna-inspect-qc

Inspect an input AnnData h5ad file and produce auditable single-cell RNA-seq quality-control evidence without modifying or filtering the source data.

Overview

Publisher	sagirimo
Repository	`BioDSH`
Skill name	`scrna-inspect-qc`
Stars	65
Forks	2
Bundled files	2
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.
2 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 Inspect Qc 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-inspect-qc
Enable the skill in any chat where you want it available.

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-inspect-qc .claude/skills/scrna-inspect-qc

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

Use it in TypingMind

Enable Scrna Inspect Qc 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 Inspect Qc 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 Inspect Qc 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 inspect and QC

Use this skill before normalization, integration, clustering, annotation, or differential expression when the input is an AnnData .h5ad file.

Required behavior

Treat the input as read-only and preserve its cell and gene order.
Report matrix shape, sparsity, annotations, layers, duplicate identifiers, non-finite or negative values, and whether values appear count-like.
Calculate per-cell and per-gene QC metrics. Detect mitochondrial genes using both human MT- and mouse mt- prefixes.
Do not silently filter cells, choose biological thresholds, normalize values, or claim that a dataset has passed QC.
Distinguish measured evidence from recommendations. Missing mitochondrial genes or metadata is a warning, not proof of invalid data.
Emit machine-readable JSON and CSV artifacts so that benchmark graders do not need to parse prose.

Outputs

dataset_profile.json: input identity, matrix characteristics, annotations, warnings, and summary quantiles.
cell_qc.csv: per-cell counts, detected genes, and mitochondrial fraction when available.
gene_qc.csv: per-gene counts and detected-cell frequency.

Bundled files

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

run.py7 KB
skill.json1 KB

Frequently asked questions

What does the Scrna Inspect Qc AI skill do?

Inspect an input AnnData h5ad file and produce auditable single-cell RNA-seq quality-control evidence without modifying or filtering the source data.

Why use Scrna Inspect Qc on TypingMind?

Because you install it once and use it with any model. Scrna Inspect Qc 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 Inspect Qc in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/sagirimo/BioDSH/tree/main/biodsh-core/skills/scrna-inspect-qc. 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 Inspect Qc?

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 Inspect Qc?

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

Is the Scrna Inspect Qc 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 inspect and QC

Required behavior

Outputs

Bundled files

Frequently asked questions

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