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 commands/herry423/celltypepilot/ctp-inspectgit clone --depth 1 https://github.com/HERRY423/CellTypePilotWhat 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 | $0.00016 | $0.00305 |
| Opus 5 | $0.00008 | $0.00152 |
| Sonnet 5 | $0.00003 | $0.00061 |
| Haiku 4.5 | $0.00002 | $0.00030 |
Grade A, and why
ctp-inspect 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.
What it actually says
CellTypePilot Inspect
Quickly understand the structure and content of a .h5ad file before annotation.
Naming note: registered as
/ctp-inspect(not/inspect) to avoid a future collision with a possible built-in/inspect(requested upstream) and to stay distinct from theclaude inspectCLI. The underlying CLI check iscelltypepilot inspect.
Instructions
-
Run inspection:
celltypepilot inspect -i <path> --json -
Review the report:
- Species auto-detection (human/mouse gene naming patterns)
- Tissue context (from obs metadata)
- Cluster keys found (leiden, louvain, etc.) with cluster counts
- Embedding keys (UMAP, tSNE, PCA)
- Layers available (counts, log-normalized, etc.)
- Gene ID convention (symbols vs Ensembl)
- Any warnings (missing embeddings, unusual gene counts, etc.)
-
Report to user: Summarize the data characteristics and confirm parameters before annotation.
Notes
- This is a read-only operation — no files are modified
- Use
--jsonfor structured output the agent can parse - If species/tissue cannot be auto-detected, ask the user before proceeding
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 · 36 lines · 16 tokens per session scan A d65d31483893
ctp-inspect is a command published in the GitHub repository HERRY423/CellTypePilot (5 stars, last pushed 9d ago), licensed MIT. It adds 16 tokens to every session and 305 once invoked, about $0.0001 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 2026-08-31.
Other commands, from other repositories
query-tcga
Query TCGA/GDC for projects, mutations, or clinical data. Use when the user asks for TCGA cohorts, mutation counts, or clinical variables from the Genomic Data Commons.
browse-files
List, search, and inspect ENCODE files by format, type, and assembly.
git
Git operations with intelligent commit messages and workflow optimization.
checklist
Generate a custom checklist for the current feature based on user requirements.
clarify
Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
specify
Create or update the feature specification from a natural language feature description.