bio-crispr-screens-jacks-analysis SKILL.md skillA
bio-crispr-screens-jacks-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-jacks-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-jacks-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,838 bytes
- Repository stars
- 662
- License
- MIT
Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not…
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: JACKS 0.2.0+ (felicityallen/JACKS), pandas 2.2+, numpy 1.26+, scipy 1.12+, matplotlib 3.8+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `python run_JACKS.py --help` (run_JACKS.py at the JACKS repo root after clone) - Python: from jacks.jacks_io import runJACKS; help(runJACKS) - GitHub: install via `git clone https://github.com/felicityallen/JACKS && cd JACKS && pip install .` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ## JACKS CRISPR Screen Analysis **"Analyze CRISPR screens with guide-level efficacy modeling"** -> Jointly model per-sgRNA log-fold-change across one or more screens as the product of gene essentiality and guide efficacy, sharing efficacy across screens with the same library so that low-quality guides are down-weighted automatically. - CLI: `python run_JACKS.py countfile replicatefile guidemappingfile [options]` (script at JACKS repo root) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-jacks-analysis@sha256:488557487f019de3The 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_zu5qvcrjyze5e7hy)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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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_zu5qvcrjyze5e7hy GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-jacks-analysis GET https://markdownregistry.com/api/v1/blob/488557487f019de31ec6a830b411fe0ab58cb1f9461c88f4562e8e44bd5d4c08
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.