Published April 24, 2023 | Version 1
Software Open

Highly multiplexed spatial analysis identifies tissue-resident memory T cells as drivers of ulcerative and immune checkpoint inhibitor induced colitis

Creators

  • 1. Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Department of Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 2. Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 3. Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 4. Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; UCyTOF.nl, Center for Molecular Medicine, University Medical Center Utrecht, Netherlands
  • 5. Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 6. Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 7. Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
  • 8. Department of Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
  • 9. Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands

Description

This R markdown document contains the code used for analysis of single-cell segmented imaging mass cytometry (IMC) data that were generated in patients with immune checkpoint inhibitor (ICI) induced or ulcerative colitis. This script was used for data normalization, data scaling, cell type annotation and single-cell analysis.

Files

IMC_analysis_pipeline.pdf

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