bio-clinical-databases-msi-detection SKILL.md skillA
bio-clinical-databases-msi-detection 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-clinical-databases-msi-detection@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-clinical-databases-msi-detection/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,070 bytes
- Repository stars
- 662
- License
- MIT
Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.
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: MSIsensor-pro 1.2+, MSIsensor 0.6+, MANTIS 1.0.5+, samtools 1.19+, mSINGS 5.6+, pandas 2.2+, cyvcf2 0.30+. FDA pembrolizumab MSI-H / dMMR pan-tumor approval is from 2017 (Le 2015 *NEJM*; KEYNOTE-016/164/158); approval extended to colorectal first-line in 2020. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. MSIsensor-pro replaces MSIsensor for tumor-only assays; MSIsensor-ct is the bTMB-equivalent for ctDNA panels. # MSI Detection; The Companion ICI Biomarker to TMB **'Detect MSI status from this somatic sequencing data'** -> Profile microsatellite instability across canonical loci (Bethesda 5 panel + extended NGS-derived sites); classify MSI-H / MSS / MSI-L per Bethesda / FDA / KEYNOTE convention. - CLI (recommended tumor-only): `msisensor-pro msi -d microsatellites.list -t tumor.bam -o msi_out -b 16` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clinical-databases-msi-detection@sha256:85a54efd8ffa57dfThe 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_pwbaykli5qg5qptl)
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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 name
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- pass: Size between 200 bytes and 200 KB (20070 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
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- 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_pwbaykli5qg5qptl GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clinical-databases-msi-detection GET https://markdownregistry.com/api/v1/blob/85a54efd8ffa57dfa1c034bae25ac549bf543ca34e976f9c1418142a91a90424
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.