TCRB matching

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Introduction: TCR Sequencing Data Processing

This repository contains scripts and functions designed to process, analyze, and link T-cell receptor (TCR) sequencing data. The focus is on comparing data generated from 10X Genomics TCR sequencing and Adaptive TRB sequencing to extract meaningful insights from TCR sequences.

Data Overview:

1. 10X TCR Sequencing Data:

   • Includes columns like 'barcode', 'chain', 'v_gene', 'j_gene', and 'raw_consensus_id'.
   • Important for understanding individual T-cell clones.

2. Adaptive TRB Sequencing Data:

   • Contains fields such as 'v_resolved', 'j_resolved', 'rearrangement', 'amino_acid', and 'productive_frequency'.
   • Useful for a broader view of the T-cell repertoire.

Key Functions:

1. treatcr(tenx_data): Processes 10X TCR sequencing data, filtering on 'TRB' chains, ensuring the V and J regions are identifiable, categorizing these regions, and counting TCR clonotypes.

2. treathvg(adap_data, sample_name='', labeled_trb=[]): Handles the Adaptive TRB sequencing data. Depending on the provided parameters, this function can focus on specific samples or labeled TCR sequences and categorizes the V and J regions.

3. link(tcr_data, hvg_data, level=1): Links the processed data from the first two functions based on either the V and J gene families (level 1) or includes their subtypes (level 2).

Workflow:

1. Process the 10X TCR sequencing data with treatcr.
2. Process the Adaptive TRB sequencing data using treathvg.
3. Establish a connection between the two processed datasets using link, culminating in the final linked dataset: tcr_sel.

Purpose:

The code enables a comprehensive comparison and integration of 10X TCR sequencing data with Adaptive TRB sequencing data, emphasizing relevant T-cell receptor sequences and their characteristics.

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