Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
Install Spatial S4 Deconvolve
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install QING1105/ezST spatial-s4-deconvolve --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .claude/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .claude/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolveType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install QING1105/ezST spatial-s4-deconvolve --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .agents/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .agents/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install QING1105/ezST spatial-s4-deconvolve --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .cursor/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .cursor/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/QING1105/ezST.git --path plugins/spatial-transcriptomics/skills/s4-deconvolve--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install QING1105/ezST spatial-s4-deconvolve --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .gemini/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .gemini/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install QING1105/ezST spatial-s4-deconvolveInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .github/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .github/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install QING1105/ezST spatial-s4-deconvolve --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s4-deconvolve .opencode/skills/spatial-s4-deconvolve && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "spatial-s4-deconvolve" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s4-deconvolve into .opencode/skills/spatial-s4-deconvolve/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s4-deconvolve", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
spatial-s4-deconvolve- GitHub stars
- 101
- Token cost
- ~480 tokens
- SKILL.md length
- 158 words
- Files
- 1
- Skills in repo
- 11
- Repo updated
- First seen
- Licence
- MIT
At a glance
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
- Works in 2 steps: DestVI (preferred):… → SPOTlight (alternative):…
- The user asks to deconvolve spatial spots
- SKILL.md covers Goal, Prerequisites, Steps and Outputs, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Spatial S4 Deconvolve is an agent skill from QING1105/ezST. 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.
Its SKILL.md is about 480 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation. The licence is MIT.
When your agent uses it
- The user asks to deconvolve spatial spots
- Estimate cell-type composition
- Run DestVI / SPOTlight with a scRNA-seq reference
Example prompts
- “/spatial-s4-deconvolve”
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- DestVI (preferred): deconvolve_spatial_destvi(ref_h5ad=..., st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=..., n_latent=…
- SPOTlight (alternative): deconvolve_spatial_spotlight(ref_h5ad=..., st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=…
What it can do on your machine
Read from SKILL.md and the folder at commit 429f9fc. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Spatial S4 Deconvolve loads about 480 tokens when it runs. Until then it costs about 80 tokens; SKILL.md has 158 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from QING1105/ezST at commit 429f9fc, republished under its MIT licence (© QING1105). 158 words, ~480 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-s4-deconvolve/SKILL.md (or your agent's skills folder).- name
- spatial-s4-deconvolve
- description
- 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.
- license
- MIT
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., columnlevel_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-toolsinstalled.
- Defaults:
- 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).
- Requires R + SPOTlight package (see
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.
© QING1105, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in plugins/spatial-transcriptomics/skills/s4-deconvolve of QING1105/ezST.
Open the folder on GitHubat commit 429f9fc
Compare with similar skills
Spatial S4 Deconvolve next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Spatial S4 Deconvolve this skillQING1105/ezST | 101 | — | ~480 | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
Similar skills
13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
More from QING1105/ezST
All 11 skills in this repoSpatial Transcriptomics
QING1105/ezST
End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
Spatial Visium Hd
QING1105/ezST
Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation.
Spatial Atera
QING1105/ezST
Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.
Spatial S3 Domains SVG
QING1105/ezST
Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.
Spatial S5 Downstream
QING1105/ezST
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
Spatial Visium
QING1105/ezST
Classic Visium platform branch of the spatial transcriptomics workflow — spot-level 5-stage pipeline (load+QC, normalize+cluster, domains+SVG, deconvolution, downstream prep).
Related
Categories
Questions about Spatial S4 Deconvolve
What does Spatial S4 Deconvolve do?
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions. Spatial S4 Deconvolve is an agent skill from QING1105/ezST. Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
When should I use Spatial S4 Deconvolve?
Spatial S4 Deconvolve fits situations like: the user asks to deconvolve spatial spots; estimate cell-type composition; run DestVI / SPOTlight with a scRNA-seq reference.
How do I install Spatial S4 Deconvolve in Claude Code?
Run `npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s4-deconvolve in QING1105/ezST) into .claude/skills/spatial-s4-deconvolve in your project. Claude Code loads it when a task matches its description.
How do I install Spatial S4 Deconvolve in Codex?
Run `npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s4-deconvolve in QING1105/ezST) into .agents/skills/spatial-s4-deconvolve in your project. Codex loads it when a task matches its description.
Can I use Spatial S4 Deconvolve in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add QING1105/ezST --skill spatial-s4-deconvolve -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spatial-s4-deconvolve, .gemini/skills/spatial-s4-deconvolve, .github/skills/spatial-s4-deconvolve and .opencode/skills/spatial-s4-deconvolve in your project.
What does Spatial S4 Deconvolve need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial S4 Deconvolve is instructions for the agent only.
Does Spatial S4 Deconvolve access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Spatial S4 Deconvolve safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Spatial S4 Deconvolve use?
Spatial S4 Deconvolve is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spatial S4 Deconvolve use?
About 480 tokens (SKILL.md is roughly 1.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Spatial S4 Deconvolve?
Skills that share tags, products or a category with Spatial S4 Deconvolve: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial S4 Deconvolve?
QING1105 (a GitHub user) maintains it in QING1105/ezST, which has 101 GitHub stars. The repository holds 11 skills in this directory. The repository was last updated on August 26, 2026.
Source: QING1105/ezST on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.