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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline.

Panwen Wang1, Yue Yu2, Haidong Dong3

  • 1Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, AZ 85259, United States.

NAR Genomics and Bioinformatics
|May 20, 2025
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Summary

This study introduces immunopipe, a tool for analyzing single-cell RNA sequencing (scRNA-seq) and single-cell T-cell receptor sequencing (scTCR-seq) data. It aids in understanding T-cell immunity and advancing immunotherapy research.

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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.