bio-crispr-screens-copy-number-correction SKILL.md skillA
bio-crispr-screens-copy-number-correction 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-copy-number-correction@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-copy-number-correction/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 18,888 bytes
- Repository stars
- 662
- License
- MIT
Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data…
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: CRISPRcleanR 3.0+ (R; github.com/francescojm/CRISPRcleanR), Chronos 2.0+ (https://github.com/broadinstitute/chronos), CERES (legacy, superseded by Chronos), pandas 2.2+, numpy 1.26+, scipy 1.12+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('CRISPRcleanR')`; `?ccr.GWclean`
- Python: `pip show crispr_chronos`; `python3 -c 'import chronos; print(chronos.__file__)'`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
## Copy-Number Bias Correction in CRISPR Screens
**"Correct copy-number artifacts in my cancer-cell-line screen"** -> Identify gene-independent depletion at amplified loci, apply CRISPRcleanR (pre-hoc, unsupervised, position-based) or Chronos (joint model, supervised with CN profile) to remove the artifact, then proceed to hit calling on corrected data.
- R: `CRISPRcleanR::ccr.GWclean()` for unsupervised pre-hoc correction (no CN profile required)
- Python: Chronos (`crispr_chronos`) for joint cell-population dynamics + CN modeling
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-copy-number-correction@sha256:69c3921645834671The 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_3hkk5ghawcfkmtju)
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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 credential-shaped string
- pass: No instruction to send local credentials anywhere
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_3hkk5ghawcfkmtju GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-copy-number-correction GET https://markdownregistry.com/api/v1/blob/69c39216458346719c5af15e25623969de3188c33dd83ffae2d5d5b36382e7d9
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.