bio-copy-number-subclonal-copy-number SKILL.md skillA
bio-copy-number-subclonal-copy-number 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-subclonal-copy-number@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-subclonal-copy-number/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 14,372 bytes
- Repository stars
- 662
- License
- MIT
Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal…
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: R 4.3+ with Battenberg 2.2.10+ and TitanCNA 1.40+, MEDICC2 1.0+, Python 3.10+; impute2/Beagle phasing reference panels.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('Battenberg')` / `'TitanCNA')` then `?function`
- CLI: `medicc2 --help`
- Battenberg is GitHub-only (`Wedge-lab/battenberg`) and needs a 1000 Genomes impute/phasing reference and allele-counter; confirm reference data is installed
Battenberg and TITAN both consume allele-specific data (logR + BAF at heterozygous SNPs); they cannot run on relative copy ratio alone.
# Subclonal Copy Number and Tumor Evolution
**"This copy number is non-integer — is it noise, or are there subclones"** -> A tumor is a mixture of cell populations. When a copy-number change is present in only some cancer cells, bulk sequencing averages it into a *non-integer* state. A long non-integer segment is not noise — it is a subclonal copy-number alteration, and resolving it reveals the tumor's clonal architecture.
- R: `Battenberg` (phased clonal + subclonal CN), `TitanCNA` (HMM mixture of cell populations)
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-subclonal-copy-number@sha256:063710a14a4a73d4The 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_jus25v3akfieb4wa)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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 (14372 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_jus25v3akfieb4wa GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-subclonal-copy-number GET https://markdownregistry.com/api/v1/blob/063710a14a4a73d4785aebcfb9d22c64f79a2349d150092eb91443a5232bf318
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.