bio-workflows-tcr-pipeline
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tcr-pipeline --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+ Before using code patterns, verify installed versions match. If versions differ: - 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. # TCR/BCR Analysis Pipeline **"Analyze my TCR/BCR repertoire sequencing data end-to-end"** → Orchestrate MiXCR clonotype extraction, VDJtools diversity/repertoire analysis, Immcantation SHM and lineage analysis, and visualization of V/J gene usage and clonal dynamics. ## Pipeline Overview ``` FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization ``` ## Step 1: MiXCR Processing ```bash # Align reads to V(D)J segments mixcr align -s hsa -p rna-seq \ R1.fastq.gz R2.fastq.gz \ aligned.vdjca # Assemble clonotypes mixcr assemble aligned.vdjca clones.clns # Export mixcr exportClones clones.clns clones.txt ``` ## Step 2: VDJtools Analysis ```bash # Convert to VDJtools format vdjtools Convert -S mixcr clones.txt vdjtools/ # Diversity metrics vdjtools CalcDiversityStats vdjtools/clones.t
- Version Compatibility
- Pipeline Overview
- Step 1: MiXCR Processing
- Step 2: VDJtools Analysis
- Step 3: Visualization
- QC Checkpoints
- Related Skills
Align reads to V(D)J segments mixcr align -s hsa -p rna-seq \ R1.fastq.gz R2.fastq.gz \ aligned.vdjca Assemble clonotypes mixcr assemble aligned.vdjca clones.clns Export mixcr exportClones clones.clns clones.txt Convert to VDJtools format vdjtools Convert -S mixcr clones.txt vdjtools/
What does the bio-workflows-tcr-pipeline skill do?
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tcr-pipeline --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.