Bio Single Cell

Organization

frumu-ai

bio-single-cell

Deep learning for single-cell analysis using scvi-tools and scverse ecosystem. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping, (7) RNA velocity with veloVI, or (8) QC analysis of single-cell RNA-seq data. Triggers include scVI, scANVI, totalVI, QC, quality control, batch correction, integration, multi-modal.

Overview

Publisher	frumu-ai
Repository	`tandem`
Skill name	`bio-single-cell`
Stars	121
Forks	13
Bundled files	Instructions only
Links	Skill source Repository Homepage

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 frumu-ai on GitHub. Read the source before you install it.

Installation

Install the Bio Single Cell 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.
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/frumu-ai/tandem/tree/main/apps/tandem-desktop/src-tauri/resources/skill-templates/bio-single-cell

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/frumu-ai/tandem.git /tmp/tandem
mkdir -p .claude/skills
cp -r /tmp/tandem/apps/tandem-desktop/src-tauri/resources/skill-templates/bio-single-cell .claude/skills/bio-single-cell

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

Use it in TypingMind

Enable Bio Single Cell 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 Bio Single Cell 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 Bio Single Cell 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.

scvi-tools Deep Learning & QC Skill

This skill provides guidance for deep learning-based single-cell analysis using scvi-tools and standard QC workflows.

Note: This skill utilizes the Bio-Informatics Pack. Scripts and references are located in: src-tauri/resources/packs/bio-informatics-pack/single-cell-analysis/

How to Use This Skill

Identify the appropriate workflow (QC or Modeling)
Use scripts in the pack's scripts/ folder
For installation or GPU issues, consult references/environment_setup.md in the pack

QC Workflow (Run First)

Before running any deep learning models, ensure data quality.

bash
# Run standard QC analysis
python src-tauri/resources/packs/bio-informatics-pack/single-cell-analysis/scripts/qc_analysis.py input.h5ad output_qc.h5ad

See references/scverse_qc_guidelines.md for detailed metrics thresholds.

Model Selection Guide

Data Type	Model	Primary Use Case
scRNA-seq	scVI	Unsupervised integration, DE, imputation
scRNA-seq + labels	scANVI	Label transfer, semi-supervised integration
CITE-seq (RNA+protein)	totalVI	Multi-modal integration, protein denoising
scATAC-seq	PeakVI	Chromatin accessibility analysis
Multiome (RNA+ATAC)	MultiVI	Joint modality analysis
Spatial + scRNA reference	DestVI	Cell type deconvolution
RNA velocity	veloVI	Transcriptional dynamics
Cross-technology	sysVI	System-level batch correction

CLI Scripts

Modular scripts for common workflows. Chain together or modify as needed.

Pipeline Scripts

Scripts are located at src-tauri/resources/packs/bio-informatics-pack/single-cell-analysis/scripts/.

Script	Purpose	Usage
`prepare_data.py`	QC, filter, HVG selection	`python prepare_data.py raw.h5ad prepared.h5ad --batch-key batch`
`train_model.py`	Train any scvi-tools model	`python train_model.py prepared.h5ad results/ --model scvi`
`cluster_embed.py`	Neighbors, UMAP, Leiden	`python cluster_embed.py adata.h5ad results/`
`differential_expression.py`	DE analysis	`python differential_expression.py model/ adata.h5ad de.csv --groupby leiden`
`transfer_labels.py`	Label transfer with scANVI	`python transfer_labels.py ref_model/ query.h5ad results/`
`integrate_datasets.py`	Multi-dataset integration	`python integrate_datasets.py results/ data1.h5ad data2.h5ad`
`validate_adata.py`	Check data compatibility	`python validate_adata.py data.h5ad --batch-key batch`

Example Workflow

bash
# Set script path
$SC_SCRIPTS = "src-tauri/resources/packs/bio-informatics-pack/single-cell-analysis/scripts"

# 1. Validate input data
python $SC_SCRIPTS/validate_adata.py raw.h5ad --batch-key batch --suggest

# 2. Prepare data (QC, HVG selection)
python $SC_SCRIPTS/prepare_data.py raw.h5ad prepared.h5ad --batch-key batch --n-hvgs 2000

# 3. Train model
python $SC_SCRIPTS/train_model.py prepared.h5ad results/ --model scvi --batch-key batch

# 4. Cluster and visualize
python $SC_SCRIPTS/cluster_embed.py results/adata_trained.h5ad results/ --resolution 0.8

Frequently asked questions

What does the Bio Single Cell AI skill do?

Why use Bio Single Cell on TypingMind?

Because you install it once and use it with any model. Bio Single Cell 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 Bio Single Cell in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/frumu-ai/tandem/tree/main/apps/tandem-desktop/src-tauri/resources/skill-templates/bio-single-cell. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Bio Single Cell?

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 Bio Single Cell?

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

Is the Bio Single Cell AI skill free?

It is published on GitHub by frumu-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

scvi-tools Deep Learning & QC Skill

How to Use This Skill

QC Workflow (Run First)

Model Selection Guide

CLI Scripts

Pipeline Scripts

Example Workflow

Frequently asked questions

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