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bio-tcr-bcr-analysis-vdjtools-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-tcr-bcr-analysis-vdjtools-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: vdjtools CalcDiversityStats, vdjtools OverlapPair, vdjtools PlotFancySpectratype.
- 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.
- java -jar vdjtools.jar <command> [options].
Source Doc
Excerpt From SKILL.md
Basic Usage
Goal: Run VDJtools commands for immune repertoire analysis.
Approach: Invoke VDJtools via Java JAR or wrapper script with appropriate subcommand and options.
## Or with wrapper script
vdjtools <command> [options]
Calculate Diversity Metrics
Goal: Compute repertoire diversity indices (Shannon, Simpson, Chao1, Gini) across samples.
Approach: Run CalcDiversityStats with a metadata file linking sample files to sample IDs and conditions.
Use cases
- Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mixcr-analysis - Generate input clonotype tables
- repertoire-visualization - Visualize VDJtools output
- immcantation-analysis - BCR-specific phylogenetics
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