Scirpy

Scirpy analyzes T cell receptor (TCR) and B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data and integrates immune-receptor information with transcriptomic profiles to characterize immune repertoires.

Key Features:

• Integration with Scanpy: Provides an extension to the Scanpy framework to integrate immune-receptor data with single-cell transcriptomic workflows.
• Data import and receptor characterization: Includes modules for efficient import of single-cell immune-receptor data and comprehensive characterization of TCRs and BCRs.
• Visualization capabilities: Offers visualization functions to explore immune repertoires at single-cell and population levels.
• Scalability: Supports analysis of large-scale single-cell sequencing datasets typical of high-throughput studies.

Scientific Applications:

• Cancer research: Enables detailed characterization of TCR repertoires and analysis of tumor-infiltrating lymphocytes within single-cell datasets.
• Infectious disease studies: Facilitates investigation of single-cell immune responses to pathogens, including applications to COVID-19 immune profiling.

Methodology:

Combines immune receptor sequencing with transcriptomic scRNA-seq data for joint analysis and provides a streamlined computational pipeline specifically tailored to TCR and BCR analysis.