bio-clinical-databases-tumor-mutational-burden SKILL.md skillA
bio-clinical-databases-tumor-mutational-burden 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-tumor-mutational-burden@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-tumor-mutational-burden/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 27,688 bytes
- Repository stars
- 662
- License
- MIT
Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA…
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: cyvcf2 0.30+, VEP 111+ (or snpEff 5.2+), pandas 2.2+, numpy 1.26+, LOHHLA 1.0+ (McGranahan 2017), DASH 1.0+ (Pyke 2022). v4.1 (May 2024) gnomAD is current for germline subtraction. Friends of Cancer Research TMB harmonization framework (Vega 2021 *Ann Oncol*) and ESMO 2024 (Mosele *Ann Oncol*) define the operational thresholds. 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. TMB calculation requires VCF with VEP / snpEff / Funcotator consequence annotations; the panel size used as denominator MUST match the assay's actual scored region, NOT the panel's total content. # Tumor Mutational Burden; Calculation, Harmonization, ICI Eligibility …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clinical-databases-tumor-mutational-burden@sha256:5c5b3f5b8dc076d6The 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_ivemw6neazkupck6)
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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: 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_ivemw6neazkupck6 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clinical-databases-tumor-mutational-burden GET https://markdownregistry.com/api/v1/blob/5c5b3f5b8dc076d6a134d6d3f119f41756598d15a3e56ae67957daa7e286c41f
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.