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TCRsift

T-cell receptor selection for TCR-T studies from antigen-specific culture and scRNA/VDJ sequencing.

Overview

TCRsift is a comprehensive pipeline for identifying antigen-specific T cell receptor clones from single-cell sequencing data. It supports:

  • Data Loading: Parse CellRanger VDJ and GEX outputs
  • CD4/CD8 Phenotyping: Classify cells based on gene expression
  • Clonotype Aggregation: Group cells by CDR3 sequences
  • Tiered Filtering: Apply biology-aware filtering to identify antigen-specific clones
  • Database Annotation: Match against VDJdb, IEDB, and CEDAR
  • TIL Matching: Find culture-validated TCRs in tumor samples
  • Sequence Assembly: Build full-length TCR sequences with constant regions

Quick Example

import tcrsift

# Load sample sheet
sample_sheet = tcrsift.load_sample_sheet("samples.yaml")

# Load samples
adata = tcrsift.load_samples(sample_sheet)

# Phenotype cells
adata = tcrsift.phenotype_cells(adata)

# Aggregate clonotypes
clonotypes = tcrsift.aggregate_clonotypes(adata)

# Filter clonotypes
filtered = tcrsift.filter_clonotypes(clonotypes, method="threshold", tcell_type="cd8")

# Annotate with VDJdb
annotated = tcrsift.annotate_clonotypes(filtered, vdjdb_path="/path/to/vdjdb")

Or via command line:

tcrsift run \
    --sample-sheet samples.yaml \
    --output-dir results/ \
    --vdjdb /path/to/vdjdb

Installation

pip install tcrsift

See Installation for detailed instructions.

Next Steps