IRProfiler

IRProfiler profiles immune receptor repertoires from high-throughput sequencing (HTS) data to quantify clonotypes, calculate V and J gene usage, and compare TR and BcR repertoires for immunogenetic analyses.

Key Features:

• Alternative Clonotype Definitions: Supports five alternative clonotype definitions to accommodate different definitions of clonality.
• Data Filtering: Implements data filtering algorithms to ensure high-quality input datasets for downstream analysis.
• Clonotype Diversity and Expression Calculation: Calculates clonotype diversity metrics and clonotype expression/abundance measures.
• V and J Gene Usage Calculation: Computes gene usage statistics for variable (V) and joining (J) subgroups.
• Comparative Clonotype Analysis: Detects shared and exclusive clonotypes among multiple repertoires for comparative studies.
• Comparative Gene Usage Analysis: Compares V and J subgroup gene usage across multiple repertoires.
• Galaxy Integration: Implemented as six tools within the Galaxy bioinformatics platform for pipeline composition.
• Scalability and Performance: Has been evaluated theoretically and experimentally for scalability with increasing dataset sizes.

Scientific Applications:

• Hematological Disorder Research: Applied in studies of diagnosis, prognostication, and monitoring of hematological disorders using immunogenetic data.
• Immune Repertoire Characterization: Used to characterize T-cell receptor (TR) and B-cell receptor (BcR) diversity from HTS datasets.
• Comparative Immunogenetics: Enables comparison of repertoires across samples or conditions to identify shared or exclusive clonotypes and gene usage patterns.

Methodology:

Data filtering; calculation of clonotype diversity and expression; gene usage calculation for V and J subgroups; support for five clonotype definitions; detection of shared and exclusive clonotypes and comparison of V/J gene usage among multiple repertoires; implemented as six tools within Galaxy.