SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data

• Shunsuke A. Sakai,

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliations Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan, Department of Radiation Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan

  https://orcid.org/0009-0002-3740-6795

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• Ryosuke Nomura,

  Roles Investigation, Methodology, Validation, Visualization, Writing – review & editing

  Affiliations Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

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• Satoi Nagasawa,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliations Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan, Department of Breast Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan

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• SungGi Chi,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliation Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan

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• Ayako Suzuki,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliation Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

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• Yutaka Suzuki,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliation Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

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• Mitsuho Imai,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliations Translational Research Support Office, National Cancer Center Hospital East, Chiba, Japan, Department of Genetic Medicine and Services, National Cancer Center Hospital East, Chiba, Japan

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• Yoshiaki Nakamura,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliations Translational Research Support Office, National Cancer Center Hospital East, Chiba, Japan, Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan

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• Takayuki Yoshino,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliations Translational Research Support Office, National Cancer Center Hospital East, Chiba, Japan, Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan

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• Shumpei Ishikawa,

  Roles Methodology, Writing – review & editing

  Affiliations Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan, Division of Pathology, National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Kashiwa, Chiba, Japan

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• Katsuya Tsuchihara,

  Roles Supervision, Writing – review & editing

  Affiliations Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

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• Shun-Ichiro Kageyama ,

  Roles Conceptualization, Supervision, Writing – review & editing

  * E-mail: riuyamas@east.ncc.go.jp (RY); skageyam@east.ncc.go.jp (SIK)

  Affiliations Department of Radiation Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan, Division of Radiation Oncology and Particle Therapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan

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• Riu Yamashita

  Roles Conceptualization, Methodology, Supervision, Writing – review & editing

  * E-mail: riuyamas@east.ncc.go.jp (RY); skageyam@east.ncc.go.jp (SIK)

  Affiliations Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

  https://orcid.org/0000-0003-0068-6949

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