CLAUDE.mdA
CLAUDE.md from engreitzlab/perturbnmf is a CLAUDE.md file: the standing instructions Claude Code reads in that repo.
mdr add engreitzlab/perturbnmf/CLAUDE.md@git:20260929.add0212Pins git:20260929.add0212 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 14 of 14 checks passed
- Kind
- CLAUDE.md file
- Repository
- engreitzlab/perturbnmf
- Path
CLAUDE.md- Versions recorded
- 5
- Latest version
- git:20260929.add0212, committed Sep 29, 2026
- First version recorded
- May 13, 2026
- Size
- 5,504 bytes
- Repository stars
- 10
- License
- MIT
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# cNMF Benchmarking Pipeline ## Overview This pipeline runs consensus Non-negative Matrix Factorization (cNMF) on single-cell perturbation data (CRISPR screens), then evaluates, calibrates, and visualizes the resulting gene programs. It runs on a single machine; the SLURM runner scripts in this repo are optional examples for an HPC cluster and must be configured for yours. ## Public repository — no project-specific content This repo is **public**. Nothing project-specific may be checked in: - No dataset, cell-line, screen, or study names, and no dated run directories (e.g. `MMDDYY_<study>_...`). - No collaborator or personal names, emails, or usernames in runnable code or docs (authorship metadata in `CITATION.cff`, `.zenodo.json`, `CHANGELOG.md`, and README fork links is fine). - No lab- or cluster-specific paths (group storage mounts, cluster scratch variables, home dirs) and no cluster-specific partitions/accounts. Use placeholders (`/path/to/...`, `<partition>`, `<your_email>`) or env vars (`PIPELINE_ROOT`, `SLURM_PARTITION`, `SLURM_MAIL_USER`). …
Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/CLAUDE.md@sha256:c04a1765b4d7729eThe line at the top of this page pins the label git:20260929.add0212, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_vmhfg74c5g66d6gu)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between May 13, 2026 and Sep 29, 2026, about one every 35 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.add0212 latest | 2026-09-29 | add0212 | 5,504 B | A | view · diff |
| git:20260810.d5289bf | 2026-08-10 | d5289bf | 4,281 B | A | view · diff |
| git:20260806.31a4992 | 2026-08-06 | 31a4992 | 4,226 B | A | view · diff |
| git:20260609.008a76e | 2026-06-09 | 008a76e | 4,205 B | A | view · diff |
| git:20260513.09a5df2 | 2026-05-13 | 09a5df2 | 3,295 B | A | view |
Audit of the latest version
- pass: Size between 200 bytes and 200 KB (5504 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vmhfg74c5g66d6gu GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/CLAUDE.md GET https://markdownregistry.com/api/v1/blob/c04a1765b4d7729ec45755f1ccfa6072c8b063f182c716ed1c06f14330be98e9
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: what a CLAUDE.md file is · keeping AGENTS.md and CLAUDE.md in sync · which agent file does what.
More from engreitzlab/perturbnmf
Every file in engreitzlab/perturbnmf