scRepertoire: An R-based toolkit for single-cell immune receptor analysis

Area of Science:

• Immunology
• Oncology
• Bioinformatics

Background:

• Single-cell sequencing enables simultaneous RNA quantification and immune cell receptor profiling.
• Existing software primarily focuses on transcriptomic data analysis, with limited options for immune receptor profiling.
• Integrating mRNA and immune profiling offers deeper biological insights.

Purpose of the Study:

• To introduce scRepertoire, an R package designed for single-cell immune receptor profiling.
• To enable seamless integration of T-cell receptor (TCR) and immunoglobulin (Ig) data with single-cell RNA sequencing.
• To provide an open-source solution for researchers in immunology and oncology.

Main Methods:

• Developed the scRepertoire R package to process 10x Genomics Chromium Immune Profiling data.
• Facilitated the analysis of both TCR and Ig enrichment workflows.
• Ensured compatibility with popular single-cell expression analysis packages like Seurat.

Main Results:

• scRepertoire effectively processes single-cell immune receptor profiling data.
• The package allows for the combined analysis of mRNA and immune receptor expression.
• Open-source availability and tutorials enhance accessibility and usability.

Conclusions:

• scRepertoire addresses the gap in software for single-cell immune receptor profiling.
• The package empowers researchers to integrate diverse single-cell data modalities.
• Open access and user-friendly tutorials promote wider adoption and research advancement.