Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.

"all public datasets analyzed in this study are available on zenodo [ 71 ] ( https://zenodo org/records/10223862 ). availability of data and materials the python package smoother tutorials and scripts used to simulate st data are publicly available on github [ 69 ] ( https://github com/jiayusupku/smoother/ ) under the bsd 3-clause license."

"smoother is publicly available as a python package ( https://github com/jiayusupku/smoother/ ).; availability of data and materials the python package smoother tutorials and scripts used to simulate st data are publicly available on github [ 69 ] ( https://github com/jiayusupku/smoother/ ) under the bsd 3-clause license.; all additional analysis scripts for reproducing results and figures presented in this study are available on github [ 70 ] ( https://github com/jiayusupku/smoother_paper/ ) under the mit license."

"Declarations Ethics approval and consent to participateNot applicable. Consent for publicationNot applicable. Competing interestsR. R. is the founder of GenoTwin and member of the Scientific Advisory Board of Diatech Pharmacogenetics and Flahy. B. I. is a consultant for or received honoraria from Volastra Therapeutics, Johnson & Johnson/Janssen, Novartis, Eisai, AstraZeneca and Merck, and has received research funding to Columbia University from Agenus, Alkermes, Arcus Biosciences, Checkmate Pharmaceuticals, Compugen, Immunocore, Regeneron, and Synthekine. None of these activities is related to the results in the current manuscript. Competing interests R. R. is the founder of GenoTwin and member of the Scientific Advisory Board of Diatech Pharmacogenetics and Flahy. B. I. is a consultant for or received honoraria from Volastra Therapeutics, Johnson & Johnson/Janssen, Novartis, Eisai, AstraZeneca and Merck, and has received research funding to Columbia University from Agenus, Alkermes, Arcus Biosciences, Checkmate Pharmaceuticals, Compugen, Immunocore, Regeneron, and Synthekine. None of these activities is related to the results in the current manuscript."

"Funding This work was funded by the National Institutes of Health, National Cancer Institute (R35CA253126, U01CA261822, and U01CA243073 to R. R. and X. F., R37CA258829 and R21CA263381 to B. I.), the Center for Integrated Cellular Analysis (RM1HG011014 to J. S. and R. R.), and the Edward P. Evans Center for MDS at Columbia University (to J. S. and R. R.). B. I. is supported by National Institute of Health grants, R37CA258829, R01CA280414, R01CA266446, U54CA274506, and additional by the Pershing Square Sohn Cancer Research Alliance Award, the Burroughs Wellcome Fund Career Award for Medical Scientists; a Tara Miller Melanoma Research Alliance Young Investigator Award; the Louis V. Gerstner, Jr. Scholars Program; and the V Foundation Scholars Award."