bio-crispr-screens-bagel-essentiality SKILL.md skillA
bio-crispr-screens-bagel-essentiality from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-crispr-screens-bagel-essentiality@git:20260726.5bc48c3Pins git:20260726.5bc48c3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bagel-essentiality/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260726.5bc48c3, committed Jul 26, 2026
- First version recorded
- May 24, 2026
- Size
- 15,319 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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 …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-crispr-screens-bagel-essentiality@sha256:f6ddc99b0bea6534The line at the top of this page pins the label git:20260726.5bc48c3, 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_ajab6ldcmec5r7b4)
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Versions
The registry has recorded 4 versions of this file, between May 24, 2026 and Jul 26, 2026, about one every 21 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260726.5bc48c3 latest | 2026-07-26 | 5bc48c3 | 15,319 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 14,785 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 14,785 B | A | view · diff |
| git:20260524.1fee1b9 | 2026-05-24 | 1fee1b9 | 14,566 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15319 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ajab6ldcmec5r7b4 GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-crispr-screens-bagel-essentiality GET https://markdownregistry.com/api/v1/blob/f6ddc99b0bea6534297e173d2f3b2dc028fee285aa54c31bd8f3582197869463
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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