tcR

tcR provides functions to analyze T cell receptor (TCR) repertoires from next-generation sequencing data, including sequence extraction and repertoire-level statistics.

Key Features:

• Primary Sequence Extraction: Extracts primary TR sequences directly from raw sequencing reads.
• Diversity Measures: Calculates diversity metrics to assess variability and richness of TCR repertoires.
• Shared Sequence Identification: Identifies shared T cell receptor sequences across samples or conditions to detect common clones or clonal expansions.
• Gene Usage Statistics: Computes gene usage statistics for TR genes, reporting frequency and distribution within samples.
• Comprehensive Analysis Methods: Implements widely used methods in TCR repertoire analysis for repertoire-level investigation.

Scientific Applications:

• Adaptive Immune Response Studies: Analyzes TCR repertoires to provide insights into antigen recognition and immune response dynamics.
• Disease Research: Supports investigation of immune responses in infections, autoimmune disorders, and cancers by characterizing repertoire changes.
• Vaccine Development: Characterizes TCR diversity and shared sequences to inform vaccine design aimed at eliciting broad and effective immune responses.

Methodology:

tcR is implemented in the R programming environment and performs primary TR sequence extraction from raw sequencing reads alongside repertoire-level computations.