scRepertoire

scRepertoire processes and analyzes single-cell T-cell receptor (TCR) and immunoglobulin (Ig) data, enabling integration of immune receptor profiling with single-cell transcriptomic workflows.

Key Features:

• Multi-format input support: The framework supports 10x, AIRR, BD, MiXCR, TRUST4, and WAT3R single-cell formats.
• Clonal analysis: Provides basic clonal analyses and repertoire summaries.
• Distance-based clustering: Includes distance-based clustering methods for immune receptor data.
• Single-cell workflow integration: Interacts with Seurat and SingleCellExperiment/Bioconductor R single-cell workflows.
• Clonotype tracking: scRepertoire 2 introduces improved workflows for clonotype tracking.
• Repertoire diversity metrics: scRepertoire 2 includes repertoire diversity metrics for immune receptor analysis.
• Visualization modules: scRepertoire 2 provides novel visualization modules for longitudinal and comparative studies.

Scientific Applications:

• Single-cell immune profiling: Couples RNA quantification with immune cell receptor profiling at the individual cell level.
• TCR and Ig enrichment analysis: Processes data derived from 10x Genomics Chromium Immune Profiling for both T-cell receptor and immunoglobulin enrichment workflows.
• Longitudinal and comparative immune studies: Facilitates tracking of immune dynamics across diverse pathophysiologic contexts in health and disease.
• Integrated transcriptomic and immune analysis: Enables end-to-end single-cell immune profiling with transcriptomic data through integration with contemporary single-cell analysis frameworks.

Methodology:

The package processes single-cell immune receptor data and integrates with Seurat and SingleCellExperiment for combined analysis with transcriptomic data. scRepertoire 2 includes performance optimizations that increased speed and reduced memory usage.