powerTCR

powerTCR models T cell receptor (TCR) clone size distributions using the Gamma-GPD spliced threshold model to quantify and compare TCR repertoires from sequencing data.

Key Features:

• R package implementation: Open-source implementation in R for analysis of TCR repertoire sequencing data.
• Gamma-GPD spliced threshold model: Implements the Gamma-GPD spliced threshold model to capture the structure of TCR frequency distributions.
• Clone size quantification: Quantifies clone size and frequency distributions within TCR repertoires.
• Stability across sequencing depths: Provides model-based estimates reported to be stable across varying sequencing depths.
• Comparative repertoire analysis: Fits theoretical models to empirical data to identify differences between individuals, conditions, or libraries.
• Biological interpretability: Produces parameters and outputs intended to be biologically interpretable for analysis of immune response landscapes.

Scientific Applications:

• Immune response studies: Enables analysis of how T cell populations and clone distributions change in immune responses.
• Disease diagnosis and treatment research: Supports investigations relating TCR repertoire features to disease states and therapeutic strategies.

Methodology:

Fits the Gamma-GPD spliced threshold model to TCR sequencing–derived frequency distributions and compares fitted model parameters across samples to quantify repertoire differences.