bio-copy-number-subclonal-copy-number
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 CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding betwe
npx skills add BioTender-max/awesome-bio-agent-skills --skill subclonal-copy-number --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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) - CLI: `medicc2` (whole-genome-d
- Version Compatibility
- Clonal vs Subclonal — What the Tools Output
- Tool Selection
- Whole-Genome Doubling — Detection and Timing
- Calling Subclonal CN with Battenberg
- Calling Subclonal CN with TITAN
- Failure Modes
- Subclonal call from insufficient depth or purity
- Mirrored subclonal allelic imbalance misread
- WGD not called — every copy number off by a factor
- Over-interpreting one subclonal segment as a subclone
- Single-region sampling misses spatial subclones
- Reconciliation
- Quantitative Thresholds
What does the bio-copy-number-subclonal-copy-number skill do?
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 CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding betwe
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill subclonal-copy-number --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.