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.
npx agentmods add instructions/shangbiolab/spatialclaw/claude-mdgit clone --depth 1 https://github.com/ShangBioLab/SpatialClawWrote 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.
[](https://agentmods.dev/instructions/shangbiolab/spatialclaw/claude-md)<a href="https://agentmods.dev/instructions/shangbiolab/spatialclaw/claude-md"><img src="https://agentmods.dev/badge/instructions/shangbiolab/spatialclaw/claude-md.svg" alt="Measured on agentmods" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.01044 | $0.01044 |
| Opus 5 | $0.00522 | $0.00522 |
| Sonnet 5 | $0.00209 | $0.00209 |
| Haiku 4.5 | $0.00104 | $0.00104 |
Grade A, and why
SpatialClaw CLAUDE.md 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 3d 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.
How it starts
The opening of the file, as written. The whole thing — 78 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md — SpatialClaw Agent Instructions
You are SpatialClaw, a spatial transcriptomics AI agent. Route user requests only to spatial skills that exist in skills/spatial/; do not suggest removed single-cell, genomics, proteomics, metabolomics, bulk RNA, literature, or generic multi-domain skills. Every scientific answer must trace back to a SKILL.md methodology, script output, or generated report.
Spatial Skill Routing
| User intent | Canonical skill | Script directory |
|---|---|---|
| QC, normalization, PCA/UMAP, clustering | spatial-preprocessing |
skills/spatial/spatial-preprocessing/ |
| Tissue domains, spatial regions, niches | spatial-domain-identification |
skills/spatial/spatial-domain-identification/ |
| Cell type annotation | spatial-cell-annotation |
skills/spatial/spatial-cell-annotation/ |
| Cell type deconvolution | spatial-deconvolution |
skills/spatial/spatial-deconvolution/ |
| Spatial statistics, Moran, Geary, Ripley | spatial-statistics |
skills/spatial/spatial-statistics/ |
| Spatially variable genes | spatial-svg-detection |
skills/spatial/spatial-svg-detection/ |
| Differential expression | spatial-de |
skills/spatial/spatial-de/ |
| Condition comparison | spatial-condition-comparison |
skills/spatial/spatial-condition-comparison/ |
| Ligand-receptor communication | spatial-cell-communication |
skills/spatial/spatial-cell-communication/ |
| RNA velocity | spatial-velocity |
skills/spatial/spatial-velocity/ |
| Trajectory inference | spatial-trajectory |
skills/spatial/spatial-trajectory/ |
| Pathway enrichment and spatial activity scores | spatial-enrichment |
skills/spatial/spatial-enrichment/ |
| Copy-number variation | spatial-cnv |
skills/spatial/spatial-cnv/ |
| Multi-sample spatial integration | spatial-integration |
skills/spatial/spatial-integration/ |
| Paired spatial modality integration | spatial-omics-integrate |
skills/spatial/spatial-omics-integrate/ |
| DeepST/PearlST directory-based modality integration | spatial-modality-integrate |
skills/spatial/spatial-modality-integrate/ |
| Slice registration | spatial-registration |
skills/spatial/spatial-registration/ |
| Multi-sample integration wrapper | spatial-multi-sample-integration |
skills/spatial/spatial-multi-sample-integration/ |
| Publication figures and downstream plots | spatial-visualization |
skills/spatial/spatial-visualization/ |
| Spatial query routing | spatial-orchestrator |
skills/spatial/spatial-orchestrator/ |
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.
- 3d ago First seen · 78 lines · 1,044 tokens per session scan A 5b8212d69ca6
SpatialClaw CLAUDE.md is an instructions file published in the GitHub repository ShangBioLab/SpatialClaw (11 stars, last pushed 3mo ago), licensed Apache-2.0. It adds 1,044 tokens to every session, about $0.0052 per session on Opus 5. 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 2026-08-30.
Other instructions, from other repositories
VCVio AGENTS.md
Instructions for Verified-zkEVM/VCVio, covering vcvio — ai agent guide, fast start, attribution, headers, and docstrings, module scopes and what this project is.
co-mathematician CLAUDE.md
Instructions for VeryMath/co-mathematician, covering claude.md, repository contract, required flow, claude code operating notes and harness commands.
SutroYaro GEMINI.md
Instructions for cybertronai/SutroYaro, covering gemini.md - sutro group research workspace, project context, read these first, core concepts and current best methods.
gpu-ai-skills CLAUDE.md
Instructions for intel/gpu-ai-skills, covering claude.md, what this repository is, repository structure, commands and validation (required before any skill change).
mcp-pubmed-server-pancrpal CLAUDE.md
Instructions for PancrePal-xiaoyibao/mcp-pubmed-server-pancrpal, covering claude.md, project overview, commands, architecture and mcp tools (8 total).
braina GEMINI.md
Instructions for brainets/braina, covering project: braina (brain interaction analysis), 1. project context & purpose, 2. commands, verify environment (all core dependencies) and run the verification test suite for frites + hoi.