Spatial S4 Deconvolve

Community

QING1105

spatial-s4-deconvolve

Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions. Use when the user asks to deconvolve spatial spots, estimate cell-type composition, or run DestVI / SPOTlight with a scRNA-seq reference. Produces cell-type proportion maps, then stops for review.

Overview

Publisher	QING1105
Repository	`ezST`
Skill name	`spatial-s4-deconvolve`
Stars	101
Forks	1
Bundled files	Instructions only
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.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by QING1105 on GitHub. Read the source before you install it.

Installation

Install the Spatial S4 Deconvolve 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/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve
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/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve

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/QING1105/ezST.git /tmp/ezST
mkdir -p .claude/skills
cp -r /tmp/ezST/plugins/spatial-transcriptomics/skills/s4-deconvolve .claude/skills/spatial-s4-deconvolve

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

Use it in TypingMind

Enable Spatial S4 Deconvolve 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 Spatial S4 Deconvolve 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 Spatial S4 Deconvolve 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.

S4 — Deconvolution

Goal

Estimate cell-type proportions for each Visium spot using a reference scRNA-seq dataset with cell-type labels.

Prerequisites

Reference scRNA-seq h5ad with cell-type labels in obs (e.g., column level_3).
Clustered Visium h5ad from S2 (or raw loaded h5ad — DestVI works on raw counts).

Steps

DestVI (preferred): deconvolve_spatial_destvi(ref_h5ad=..., st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=..., n_latent=..., max_epochs=..., destvi_max_epochs=...)
- Defaults: n_latent=30, max_epochs=400 (CondSCVI), destvi_max_epochs=500.
- Requires scvi-tools installed.
SPOTlight (alternative): deconvolve_spatial_spotlight(ref_h5ad=..., st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=..., r_script_path=...)
- Requires R + SPOTlight package (see install_r_packages_spatial.R).

Outputs

results/07_deconvolution/<sample>_proportions.csv (spots × cell types)
results/07_deconvolution/<sample>_proportions_*.png (spatial proportion maps, stacked bar)

Biological Interpretation

Report dominant cell types and their spatial localization.
Cross-check with tissue type: e.g., gastric cancer should show epithelial/tumor cells in tumor regions, immune cells at infiltrate margins.
Flag any surprising dominant cell type (e.g., >50% of a cell type not expected in the tissue).

Stop for Review

Present interpretation using the template from the parent spatial-transcriptomics skill. Wait for 通过 / 调整 / 跳过 before proceeding to S5.

Frequently asked questions

What does the Spatial S4 Deconvolve AI skill do?

Why use Spatial S4 Deconvolve on TypingMind?

Because you install it once and use it with any model. Spatial S4 Deconvolve 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 Spatial S4 Deconvolve in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Spatial S4 Deconvolve?

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 Spatial S4 Deconvolve?

As many as you like. As long as a model supports skills, you can use Spatial S4 Deconvolve with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Spatial S4 Deconvolve AI skill free?

Yes. It is published on GitHub by QING1105 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

S4 — Deconvolution

Goal

Prerequisites

Steps

Outputs

Biological Interpretation

Stop for Review

Frequently asked questions

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