bio-crispr-screens-hit-calling SKILL.md skillA
bio-crispr-screens-hit-calling from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-crispr-screens-hit-calling@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-crispr-screens-hit-calling/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 19,522 bytes
- Repository stars
- 662
- License
- MIT
Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK…
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
## Version Compatibility Reference examples tested with: MAGeCK 0.5.9+, BAGEL2 2.0, drugZ Aug 2019+, JACKS 0.2.0+, Chronos 2.0+ (DepMap), CERES 1.0+, pandas 2.2+, numpy 1.26+, scipy 1.12+, statsmodels 0.14+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `mageck --version`, `BAGEL.py version`, `python drugz.py --help` - Python: `pip show crispr_chronos` (JACKS installs from GitHub, not PyPI) If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ## Hit Calling Decision Tree **"Identify significant hits in my CRISPR screen"** -> Choose the analysis method that matches the experimental design, statistical assumptions, and quality grade of the screen. Reconcile across methods when high-stakes hits must be validated. The primary hit-calling methods cover non-overlapping niches; the decision is not "which is best" but "which matches the design." | Design / question | Primary method | Why | Secondary check | |--------------------|----------------|-----|------------------| …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-hit-calling@sha256:a3470a5113e3f0b4The line at the top of this page pins the label git:20260821.2d1b678, 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_subwy7yhew64pupi)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_subwy7yhew64pupi GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-hit-calling GET https://markdownregistry.com/api/v1/blob/a3470a5113e3f0b4dc0505a0672ce271e72984204fa241ac4a831e603e1ef85a
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: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.