How do I install the Bio Workflows Tcr Pipeline skill?

Run npx skillmds@latest add gabrielmoreira/bio-workflows-tcr-pipeline in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bio Workflows Tcr Pipeline safe to use?

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Which AI agents work with Bio Workflows Tcr Pipeline?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bio Workflows Tcr Pipeline free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bio Workflows Tcr Pipeline?

gabrielmoreira (@gabrielmoreira) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bio Workflows Tcr Pipeline by gabrielmoreira

Name: Bio Workflows Tcr Pipeline
Rating: 4.2 (5 reviews)
Author: gabrielmoreira

File contents

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

# 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

# Convert to VDJtools format
vdjtools Convert -S mixcr clones.txt vdjtools/

# Diversity metrics
vdjtools CalcDiversityStats vdjtools/clones.txt diversity/

# Sample overlap
vdjtools CalcPairwiseDistances vdjtools/*.txt overlap/

Step 3: Visualization

# Spectratype plot
vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/

# V usage
vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/

QC Checkpoints

After alignment: Check V/J assignment rate (>70% typical)
After assembly: Verify clonotype count and coverage
After diversity: Compare metrics to expected range

Related Skills

tcr-bcr-analysis/mixcr-analysis - Detailed MiXCR usage
tcr-bcr-analysis/vdjtools-analysis - Diversity metrics
tcr-bcr-analysis/repertoire-visualization - Plots

---name: bio-workflows-tcr-pipelinedescription: 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.--- ## 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.txt diversity/ # Sample overlap vdjtools CalcPairwiseDistances vdjtools/*.txt overlap/ ``` ## Step 3: Visualization ```bash # Spectratype plot vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/ # V usage vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/ ``` ## QC Checkpoints 1. **After alignment**: Check V/J assignment rate (>70% typical) 2. **After assembly**: Verify clonotype count and coverage 3. **After diversity**: Compare metrics to expected range ## Related Skills - tcr-bcr-analysis/mixcr-analysis - Detailed MiXCR usage - tcr-bcr-analysis/vdjtools-analysis - Diversity metrics - tcr-bcr-analysis/repertoire-visualization - Plots

Frequently asked questions

Bio Workflows Tcr Pipeline