bio-crispr-screens-base-editing-analysis SKILL.md skillA
bio-crispr-screens-base-editing-analysis 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-base-editing-analysis@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-base-editing-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 23,481 bytes
- Repository stars
- 662
- License
- MIT
Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic…
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: CRISPResso2 2.2.14+, BE-Hive 1.0+ (BE prediction), pandas 2.2+, biopython 1.83+, numpy 1.26+, scipy 1.12+, scikit-learn 1.4+; Broad be-validation-pipeline notebooks (repo HEAD). Before using code patterns, verify installed versions match. If versions differ: - CLI: `CRISPResso --version` - Python: `pip show CRISPResso2`; BE-Hive is a GitHub clone (maxwshen/be_predict_bystander), not a PyPI package If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ## Base Editing Screen Analysis **"Analyze my base-editor variant-function screen"** -> Quantify per-sgRNA target-base conversion, bystander rate, and indel byproducts from amplicon sequencing; filter on editing efficiency; map each sgRNA to its intended SNV (target + bystander pattern); compute per-variant fitness from the screen log-fold change; reconcile target vs bystander variant attribution; annotate against ClinVar / COSMIC. - CLI: `CRISPResso --base_editor_output` for per-amplicon BE quantification …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-base-editing-analysis@sha256:dcffe0aa4a886ebbThe 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_7rdzojahqdhbgjds)
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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: Size between 200 bytes and 200 KB (23481 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7rdzojahqdhbgjds GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-base-editing-analysis GET https://markdownregistry.com/api/v1/blob/dcffe0aa4a886ebbdd09404d2ece77a38cd16b66ed7385e78a986a180872e4d3
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.
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