bio-copy-number-cnv-annotation SKILL.md skillA
bio-copy-number-cnv-annotation 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-copy-number-cnv-annotation@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-copy-number-cnv-annotation/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 13,925 bytes
- Repository stars
- 662
- License
- MIT
Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event…
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: bedtools 2.31+, AnnotSV 3.4+, Python 3.10+ with pybedtools 0.9+, pandas 2.2+, pysam 0.22+; R 4.3+ with clusterProfiler 4.10+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `bedtools --version`, `AnnotSV --version`
- Python: `pip show pybedtools pandas pysam`
- R: `packageVersion('clusterProfiler')`
If code throws an error, introspect the installed package and adapt the example. AnnotSV output column names change between major versions — verify against the installed version.
# CNV Annotation
**"Annotate my CNV calls with the genes they affect"** -> Overlap CNV segments with gene models, dosage-sensitivity maps, and clinical databases. The hard part is not the intersection — it is deciding *which* genes matter. A focal amplification overlapping 30 genes usually has one driver (the peak gene); a deletion's consequence depends on whether each gene is dosage-sensitive and whether the whole gene or only part is removed.
- CLI: `bedtools intersect -a cnvs.bed -b genes.bed -wa -wb`; `AnnotSV` for full annotation
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-cnv-annotation@sha256:c9ede44472d8c553The 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_hjwq43fjmbigvvci)
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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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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_hjwq43fjmbigvvci GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-cnv-annotation GET https://markdownregistry.com/api/v1/blob/c9ede44472d8c5537ae30fc967cba70205de774f851a0f4c424230b02b6fdca4
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.