bio-tcr-bcr-analysis-mixcr-analysis
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-mixcr-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+, pandas 2.2+ 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. # MiXCR Analysis **"Extract TCR/BCR clonotypes from my sequencing data"** → Assemble immune receptor sequences from raw reads, identify V(D)J gene segments, and generate clonotype tables for repertoire analysis. - CLI: `mixcr analyze` for end-to-end TCR/BCR extraction and clonotype assembly ## Complete Workflow (Recommended) **Goal:** Run end-to-end V(D)J alignment and clonotype assembly from raw FASTQ files in a single command. **Approach:** Use MiXCR's preset-based `analyze` command which chains alignment, assembly, and export steps automatically. ```bash mixcr analyze generic-tcr-amplicon \ --species human \ --rna \ --rigid-left-alignment-boundary \ --floating-right-alignment-boundary C \ input_R1.fastq.gz input_R2.fastq.g
- Version Compatibility
- Complete Workflow (Recommended)
- Step-by-Step Workflow
- Step 1: Align Reads
- Step 2: Refine and Assemble
- Step 3: Export Results
- Preset Protocols
- Species Support
- Output Format
- Quality Metrics
- Parse MiXCR Output in Python
- Related Skills
mixcr analyze generic-tcr-amplicon \ input_R1.fastq.gz input_R2.fastq.gz \ output_prefix mixcr analyze 10x-vdj-tcr \ mixcr align \ alignments.vdjca mixcr refineTagsAndSort alignments.vdjca alignments_refined.vdjca mixcr assemble alignments_refined.vdjca clones.clns mixcr exportClones \ clones.clns \
What does the bio-tcr-bcr-analysis-mixcr-analysis skill do?
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-mixcr-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.