immLynx

immLynx bridges popular Python-based immune repertoire analysis tools and Hugging Face protein language models into the R environment, providing unified interfaces for single-cell TCR analysis.

Key Features:

• TCR Distance Calculations: Provides unified interface for tcrdist3 to calculate TCR distances.
• Sequence Generation Probability: Provides unified interface for OLGA to compute sequence generation probabilities.
• Selection Inference: Provides unified interface for soNNia to infer selection pressures.
• Clustering: Provides unified interface for clusTCR to perform TCR sequence clustering.
• Protein Embeddings: Provides unified interface for ESM-2 to generate protein embeddings.
• Metaclone Discovery: Provides unified interface for metaclonotypist to identify metaclonotypes.
• Ecosystem Compatibility: Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.

Scientific Applications:

• Single-Cell Immune Repertoire Analysis: Integrates Python-based TCR analysis tools and protein language models within R-based single-cell workflows.

Methodology:

immLynx provides unified R interfaces that wrap Python-based immune repertoire analysis tools and Hugging Face protein language models.