Spatial Transcriptomics

What it does

When your agent uses it

• The user asks to analyze Visium / spatial transcriptomics data
• Run spatial analysis pipelines (load
• Spatial domains
• Neighborhood enrichment

Example prompts

• “/spatial-transcriptomics”

Requirements

• Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

1. 1Run the tool chain for that stage, producing plots (PNG) and result files.
2. 2Interpret the outputs with the vision tool (for plots) and by reading result files. Write a biological interpretation using the template…
3. 3Stop and present the interpretation + plots to the user.
4. 4Wait for review. The user chooses one of: 通过 (proceed), 调整 (adjust parameters and rerun this stage), or 跳过 (skip this stage and continue).

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

  Shell commands in SKILL.md call:

  • python
  • pip

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

  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 Transcriptomics loads about 1.4k tokens when it runs. Until then it costs about 136 tokens; SKILL.md has 566 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~136

When it runs · the whole SKILL.md, loaded when a task matches

~1.4k

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

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). 566 words, ~1,422 tokens.

name

spatial-transcriptomics

description

End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates. Use when the user asks to analyze Visium / spatial transcriptomics data, run spatial analysis pipelines (load, QC, normalize, cluster, spatial domains, SVG, deconvolution, neighborhood enrichment, cell-cell communication), or interpret spatial plots biologically. Each stage produces plots and results, the LLM interprets their biological meaning, then stops and waits for the user's review before proceeding.

license

MIT

# Check critical Python packages
python -c "import scanpy, squidpy, scvi, leidenalg; print('OK')"
# Check critical R packages (only needed for S4/S5)
Rscript -e "library(Seurat); library(SPOTlight); library(CellChat); cat('OK\n')"

【S{n} 阶段结果】
- 关键数字：XXX spots retained / XXX clusters / XXX spatial domains / top cell types...
- 图片观察：图中可见……（描述 spatial pattern, e.g., 高表达区域聚集在左上象限）
- 生物学意义：这提示……（e.g., 该区域可能是肿瘤浸润边缘，富集免疫细胞通讯）
- 建议：是否调整参数 / 进入下一阶段

© 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/spatial-transcriptomics of QING1105/ezST.

Open the folder on GitHubat commit 429f9fc