Borrowing it
Nothing to install: this file belongs to HERRY423/CellTypePilot. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/HERRY423/CellTypePilot/main/AGENTS.mdgit clone --depth 1 https://github.com/HERRY423/CellTypePilotWrote 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/herry423/celltypepilot/agents-md)<a href="https://agentmods.dev/instructions/herry423/celltypepilot/agents-md"><img src="https://agentmods.dev/badge/instructions/herry423/celltypepilot/agents-md/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.
<a href="https://agentmods.dev/instructions/herry423/celltypepilot/agents-md"><img src="https://agentmods.dev/badge/instructions/herry423/celltypepilot/agents-md.svg" alt="Reviewed on agentmods" width="80" 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 5.1 | $0.04451 | $0.04451 |
| Opus 5.5 | $0.01780 | $0.01780 |
| Sonnet 5.5 | $0.00890 | $0.00890 |
| Haiku 4.5 | $0.00445 | $0.00445 |
Grade A, and why
CellTypePilot AGENTS.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 1mo 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 — 319 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CellTypePilot — Codex Agent Instructions
Single-cell annotation plugin with evidence, conservative abstention, and reviewable draft output.
When to use
Activate CellTypePilot when the user wants to:
- Annotate, label, or identify cell types in pre-clustered scRNA-seq / spatial data
- Work with
.h5adfiles containing clustered single-cell data - Convert Seurat
.rdsfiles to.h5adfor analysis - Understand "what are these clusters?"
- Get auditable draft cell-type annotations with evidence for human review
- Review annotations interactively in a web panel
Trigger phrases: "annotate my clusters", "what cell types are these?", "label my scRNA-seq", "figure out the cell types", "run celltypepilot", "annotate my h5ad", "convert my rds", "review annotations in browser".
Prerequisites
Before running anything, verify the environment:
celltypepilot doctor
If core dependencies are missing, install them:
pip install celltypepilot
For a repository checkout used in development, pip install -e . remains appropriate.
CellTypePilot runs on CPU, requires Python >= 3.10, scanpy, anndata, and matplotlib. No MCP servers, no pixi, no conda environment needed for the basic path.
Optional extras:
pip install "celltypepilot[web]"— Web Inspector (Flask-based interactive review panel)pip install "celltypepilot[mcp]"— Native local CellTypePilot MCP facade for Agent hostspip install "celltypepilot[seurat]"— Seurat .rds conversion (requires rpy2 or R)pip install "celltypepilot[native]"— CellTypist, scANVI, popV (Python 3.12+), and bounded LLM Python runtimespip install "celltypepilot[all]"— All optional features
SingleR additionally requires R with the Bioconductor packages SingleR, zellkonverter,
scuttle, and SummarizedExperiment. CHETAH requires R with CHETAH, zellkonverter,
SummarizedExperiment, and SingleCellExperiment. CellAssign requires R with cellassign,
zellkonverter, and SummarizedExperiment, plus a frozen binary marker matrix.
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.
- 1mo ago First seen · 319 lines · 4,451 tokens per session scan A e40148f9f289
CellTypePilot AGENTS.md is an instructions file published in the GitHub repository HERRY423/CellTypePilot (5 stars, last pushed 1mo ago), licensed MIT. It adds 4,451 tokens to every session, about $0.0178 per session on Opus 5.5. 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 instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).