bio-crispr-screens-bagel-essentiality SKILL.md skillA
bio-crispr-screens-bagel-essentiality 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-bagel-essentiality@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-bagel-essentiality/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- 15,553 bytes
- Repository stars
- 638
- License
- MIT
Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity…
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: BAGEL2 2.0 (hart-lab/bagel, build 115), pandas 2.2+, numpy 1.26+, scipy 1.12+, matplotlib 3.8+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `BAGEL.py fc --help`; `BAGEL.py bf --help`; `BAGEL.py pr --help` - Python: BAGEL2 is distributed via `git clone` (no canonical PyPI release); confirm `BAGEL.py version` after checkout. If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ## BAGEL2 Essentiality Analysis **"Identify essential genes from my CRISPR fitness screen using BAGEL2"** -> Compute per-sgRNA fold changes from counts, derive per-gene log-likelihood ratios against reference essential and non-essential gene sets, sum to Bayes Factor, and apply BF threshold calibrated by precision-recall against the reference. - CLI: `BAGEL.py fc` to compute fold changes - CLI: `BAGEL.py bf` to compute Bayes Factors - CLI: `BAGEL.py pr` for precision-recall curves - Reference sets: CEGv2 (essentials) and NEGv1 (non-essentials); both at https://github.com/hart-lab/bagel …
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How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-bagel-essentiality@sha256:0ef1b27049adc0d0The 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_olidfrxxhe2zunt6)
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 638 stars · license MIT · pushed 2026-10-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_olidfrxxhe2zunt6 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-bagel-essentiality GET https://markdownregistry.com/api/v1/blob/0ef1b27049adc0d06d3b4d368f0a47004d237505dfb93636bf600d2a1e330713
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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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