Abstract 4959: Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline
Authors: Wang Panwen , Dong Haidong , Yu Yue , Zhang Shuwen , Sun Zhifu , Kocher Jean-Pierre A. , Wang Junwen , Yi Lin , Li Ying 
Published: March 2024

Abstract
Introduction: Single-cell RNA-sequencing (scRNA-seq) pairing with single-cell T-Cell-Receptor-sequencing (scTCR-seq) enables profiling of gene expression and TCR repertoires in individual T cells, elevating our understanding of T-cell-mediated immunity. Here, we present immunopipe, a comprehensive and flexible pipeline (https://github.com/pwwang/immunopipe) for analyzing the paired data. Besides the command-line tool, it offers a user-friendly web interface that allows users with varying programming expertise to configure, initiate, and monitor the pipeline. By combining extensive functionality with ease of use, immunopipe empowers users to unlock valuable insights from the data, which notably advances our understanding of immune response and fosters the development of innovative immunotherapies.
Results: Immunopipe is a comprehensive analytical pipeline for scRNA-seq and scTCR-seq data, offering various modules leveraging existing tools and novel methods to ensure data quality and enable downstream analytics. It performs quality control for scRNA-seq data, clusters cells based on gene expression to facilitate the identification of cell populations and provides insights into T-cell heterogeneity and functional diversity through T-cell selection and clustering. Enrichment analysis identifies markers and pathways for T-cell characterization. Our automated T-cell annotation tool annotates cell types accurately and hierarchically. For scTCR-seq data, immunopipe analyzes TCR clones, including clonality, diversity, gene usage, and repertoire overlap. Clone residency analysis examines the presence of clones across samples. Integrative analyses combine scRNA-seq and scTCR-seq data, providing a comprehensive understanding of the cellular landscape. Immunopipe incorporates diverse cell group information to analyze T-cell populations, which enables granular perspectives of the data for comprehensive insights. Immunopipe offers a flexible platform, allowing users to customize the analyses as needed. It supports both core and optional analyses through configuration, where users have control over the adjustable parameters. The pipeline relies on cell grouping information that can be referenced from metadata or modified to generate new variables for analysis and data filtering. Immunopipe can be executed locally or on scheduler platforms, and a docker image is provided for compatibility and simplified installation. It also offers a web interface that facilitates configuration, execution monitoring, and access to results.
Conclusion: Immunopipe is a flexible and user-friendly pipeline for analyzing scRNA-seq and scTCR-seq data. It empowers researchers to gain valuable insights that could enhance the understanding of immune responses and facilitate the development of innovative immunotherapies.
Citation Format: Panwen Wang, Haidong Dong, Yue Yu, Shuwen Zhang, Zhifu Sun, Jean-Pierre A. Kocher, Junwen Wang, Lin Yi, Ying Li. Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4959.