CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments

• Zachary Hemminger,

  Roles Conceptualization, Formal analysis, Methodology, Software, Writing – original draft

  Affiliation Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America

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• Haley De Ocampo,

  Roles Investigation

  Affiliation Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America

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• Fangming Xie,

  Roles Software

  Affiliation Department of Chemical Biology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America

  https://orcid.org/0000-0001-5232-1648

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• Zhiqian Zhai,

  Roles Software

  Affiliation Department of Statistics and Data Science, University of California, Los Angeles, California, United States of America

  https://orcid.org/0009-0001-3104-7472

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• Jingyi Jessica Li,

  Roles Funding acquisition, Supervision

  Affiliations Department of Statistics and Data Science, University of California, Los Angeles, California, United States of America, Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America

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• Roy Wollman

  Roles Conceptualization, Formal analysis, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: rwollman@ucla.edu

  Affiliations Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America, Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America, Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America

  https://orcid.org/0000-0003-3865-2605

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