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Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

Kaishu Mason, Anuja Sathe, Paul Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Hanlee P. Ji, Nancy Zhang
doi: https://doi.org/10.1101/2023.01.03.522646
Kaishu Mason
1Department of Statistics and Data Science, The Wharton School, University of Pennsylvania
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Anuja Sathe
2Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Paul Hess
1Department of Statistics and Data Science, The Wharton School, University of Pennsylvania
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Jiazhen Rong
3Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania
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Chi-Yun Wu
4The Gladstone Institute
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Emma Furth
5Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
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Hanlee P. Ji
2Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Nancy Zhang
1Department of Statistics and Data Science, The Wharton School, University of Pennsylvania
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  • For correspondence: nzh@wharton.upenn.edu
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Article Information

doi 
https://doi.org/10.1101/2023.01.03.522646
History 
  • January 4, 2023.
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

Author Information

  1. Kaishu Mason1,
  2. Anuja Sathe2,
  3. Paul Hess1,
  4. Jiazhen Rong3,
  5. Chi-Yun Wu4,
  6. Emma Furth5,
  7. Hanlee P. Ji2 and
  8. Nancy Zhang1,⍰
  1. 1Department of Statistics and Data Science, The Wharton School, University of Pennsylvania
  2. 2Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
  3. 3Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania
  4. 4The Gladstone Institute
  5. 5Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
  1. ↵⍰Email: nzh{at}wharton.upenn.edu
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Posted January 04, 2023.
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Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Kaishu Mason, Anuja Sathe, Paul Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Hanlee P. Ji, Nancy Zhang
bioRxiv 2023.01.03.522646; doi: https://doi.org/10.1101/2023.01.03.522646
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Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Kaishu Mason, Anuja Sathe, Paul Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Hanlee P. Ji, Nancy Zhang
bioRxiv 2023.01.03.522646; doi: https://doi.org/10.1101/2023.01.03.522646

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