Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline

Area of Science:

• Immunology
• Bioinformatics
• Genomics

Background:

• Single-cell sequencing provides high-resolution cellular data.
• Simultaneous profiling of scRNA-seq and scTCR-seq is crucial for understanding T-cell immunity.
• Advancing immunotherapy requires integrated analysis of immune cell heterogeneity and T-cell receptor repertoires.

Purpose of the Study:

• To present immunopipe, a comprehensive and flexible pipeline for integrated analysis of scRNA-seq and scTCR-seq data.
• To offer a user-friendly web interface alongside a command-line tool for broader accessibility.
• To empower researchers in uncovering insights into immune responses and immunotherapy.

Main Methods:

• Development of a bioinformatics pipeline integrating scRNA-seq and scTCR-seq data analysis.
• Implementation of both command-line and web-based interfaces for pipeline execution.
• Focus on analyzing cell heterogeneity and T-cell receptor repertoires.

Main Results:

• The immunopipe pipeline enables simultaneous exploration of cell heterogeneity and T-cell receptor repertoires.
• The integrated analysis facilitates a deeper understanding of T-cell-mediated immunity.
• The pipeline supports researchers without extensive programming experience through its web interface.

Conclusions:

• Immunopipe provides a powerful and accessible tool for integrated scRNA-seq and scTCR-seq data analysis.
• This approach enhances the understanding of immune responses.
• The pipeline facilitates advancements in immunotherapy development.