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analyze-spatial

analyze-spatial is a command for Claude Code from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (342 once invoked), scanned A, original, MIT.

A command for analysing spatial transcriptomics data, which measures gene activity together with where cells or tissue regions are located. It supports Visium, Xenium, MERSCOPE, and CosMx data.

In plain words
What is it for?
Use it to load data, check spatial quality, find genes that vary by location, estimate cell mixtures, and assign tissue domains or niches.
Why use it?
It helps avoid interpreting different measurement types in the same way, such as treating a Visium spot containing several cells as one cell. It also calls for spatial quality checks, segmentation checks, and ranked spatially variable genes.

Command for Claude Code

Written for Claude Code: allowed-tools in frontmatter. Also seen: positional $N argument.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to load data, check spatial quality, find genes that vary by location, estimate cell mixtures, and assign tissue domains or niches.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/zamushwani/biomedical-ai-skills/analyze-spatial
View source ↗ zamushwani/biomedical-ai-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for analyze-spatial

README.md
[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/analyze-spatial/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/analyze-spatial)
Your own site
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/analyze-spatial"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/analyze-spatial/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for analyze-spatial

Your own site · 80×15
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/analyze-spatial"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/analyze-spatial.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 342 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.00342
Opus 5.5 $0.00000 $0.00137
Sonnet 5.5 $0.00000 $0.00068
Haiku 4.5 $0.00000 $0.00034

Measured 2mo ago against content hash dcecc5344986, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

analyze-spatial scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/commands/analyze-spatial.md · 28 lines

What it actually says

Analyse the spatial data at $0 from platform $1.

Follow the spatial-transcriptomics skill. Platform determines almost everything:

Visium        spots, not cells. Each spot is a mixture -> deconvolution required.
Visium HD     2um bins; binning choice changes the analysis.
Xenium/CosMx  true single cells, but a targeted panel -> absent != not expressed.
MERSCOPE      single cells, panel-limited, segmentation-sensitive.

The parts that are usually got wrong:

  1. QC spatially, not just per-cell. A low-count region can be biology (necrosis) or a tissue fold. A global count filter erases both without distinction.
  2. Do not report a Visium spot as a cell. Deconvolve, and say which reference was used.
  3. Rank spatially variable genes, do not just FDR-filter them. With thousands of genes almost everything is "significant"; the ranking is the result.
  4. For imaging platforms, check segmentation before trusting per-cell counts — over-segmentation splits one cell into two low-count cells.

Report: platform-appropriate QC, SVGs with their ranking statistic, and domain/niche assignments with the method named.

If $0 is empty, ask for the data path.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 28 lines · 0 tokens per session scan A dcecc5344986

Subscribe to this mod's changes

analyze-spatial is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 342 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Analytics and metricsDESeq2Scientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

analyze-spatial compared with commands from other repositories

analyze-spatial next to 6 commands from other repositories
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analyze-spatialzamushwani/biomedical-ai-skillsCommand11mo agoMITA0Claude Code
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criticHERRY423/CellTypePilotCommand62mo agoMITA14Claude Code
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