bio-tcr-bcr-analysis-vdjtools-analysis
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-vdjtools-analysis --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: MiXCR 4.6+, VDJtools 1.2.1+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+ 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` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # VDJtools Analysis **"Compute diversity and overlap for my TCR repertoires"** → Calculate repertoire diversity metrics, sample overlap, and perform statistical comparisons between immune repertoire samples. - CLI: `vdjtools CalcDiversityStats`, `vdjtools OverlapPair`, `vdjtools PlotFancySpectratype` ## Basic Usage **Goal:** Run VDJtools commands for immune repertoire analysis. **Approach:** Invoke VDJtools via Java JAR or wrapper script with appropriate subcommand and options. ```bash # VDJtools requires Java java -jar vdjtools.jar <command> [options] # Or with wrapper script vdjtools <command> [options] ``` ## Calculate Diversity Metrics **Goal:** Compute repertoire diversity
- Version Compatibility
- Basic Usage
- Calculate Diversity Metrics
- Diversity Metrics Explained
- Sample Comparison
- Spectratype Analysis
- Clonal Tracking
- Input Format
- Convert from MiXCR
- Parse VDJtools Output in Python
- Related Skills
VDJtools requires Java java -jar vdjtools.jar <command> [options] Or with wrapper script vdjtools <command> [options] Basic diversity (Shannon, Simpson, Chao1, etc.) vdjtools CalcDiversityStats \ output_dir/ Metadata format (tab-separated): sample1.txt S1 control sample2.txt S2 treated
What does the bio-tcr-bcr-analysis-vdjtools-analysis skill do?
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-vdjtools-analysis --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.