Analyze T-cell receptor (TCR) and B-cell receptor (BCR) repertoires from bulk or single-cell sequencing data for immunology research, vaccine development, and cancer immunotherapy.
Tool type: mixed | Primary tools: MiXCR, VDJtools, Immcantation, scirpy
| Skill | Description |
|---|---|
| mixcr-analysis | V(D)J alignment and clonotype assembly from sequencing data |
| vdjtools-analysis | Repertoire diversity metrics and sample comparison |
| immcantation-analysis | BCR phylogenetics and somatic hypermutation analysis |
| scirpy-analysis | Single-cell TCR/BCR analysis with Scanpy integration |
| repertoire-visualization | Clone tracking, diversity plots, and network visualization |
- "Assemble TCR clonotypes from my FASTQ files"
- "Calculate Shannon diversity and clonality for my repertoire"
- "Find shared clonotypes between samples"
- "Analyze BCR somatic hypermutation patterns"
- "Integrate VDJ data with my scRNA-seq analysis"
- "Track clonal expansion between timepoints"
- "Create a circos plot of V-J gene usage"
# MiXCR
conda install -c bioconda mixcr
# VDJtools (requires Java)
wget https://github.com/mikessh/vdjtools/releases/download/1.2.1/vdjtools-1.2.1.zip
unzip vdjtools-1.2.1.zip
# Immcantation (R)
install.packages(c('alakazam', 'shazam', 'tigger', 'dowser'))
# scirpy (Python)
pip install scirpy mudata- single-cell - scRNA-seq analysis with VDJ enrichment
- metagenomics - Immune profiling in metagenomic samples
- phylogenetics - Tree reconstruction concepts