bio-crispr-screens-mageck-analysis SKILL.md skillA
bio-crispr-screens-mageck-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-mageck-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-mageck-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 24,083 bytes
- Repository stars
- 662
- License
- MIT
Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices…
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: MAGeCK 0.5.9+, MAGeCKFlute 2.0+ (R/Bioconductor), MAGeCK-VISPR 0.5.6+, pandas 2.2+, numpy 1.26+, matplotlib 3.8+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `mageck --version`, `mageck count --help`, `mageck test --help`, `mageck mle --help`
- R: `packageVersion('MAGeCKFlute')`, `?FluteRRA`, `?FluteMLE`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
## MAGeCK CRISPR Screen Analysis
**"Run MAGeCK on my pooled CRISPR screen"** -> Count sgRNAs from FASTQ, normalize across samples, and rank genes by enrichment or depletion using either the robust rank aggregation (RRA) test for two-condition designs or the maximum-likelihood (MLE) model with explicit design matrix for multi-condition / time-course / drug screens.
- CLI: `mageck count` -> `mageck test` for two-condition RRA
- CLI: `mageck mle` for multi-condition / time-course / multi-cell-line MLE
- R: `MAGeCKFlute::FluteRRA()` / `FluteMLE()` for downstream visualization and pathway analysis
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-mageck-analysis@sha256:1d0291e5b92dd8eeThe 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_etcgqg6jwgjr66hz)
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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: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (24083 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_etcgqg6jwgjr66hz GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-mageck-analysis GET https://markdownregistry.com/api/v1/blob/1d0291e5b92dd8ee2560470619e05021eb01ccfb041b67c645e129f29ba094f4
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.