spacedeconv: deconvolution of tissue architecture from spatial transcriptomics

spacedeconv: deconvolution of tissue architecture from spatial transcriptomics | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article spacedeconv: deconvolution of tissue architecture from spatial transcriptomics Constantin Zackl, Maria Zopoglou, Reto Stauffer, Markus Ausserhofer, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5102166/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Investigating tissue architecture is key to understanding tissue function in health and disease. While spatial omics technologies enable the study of cell transcriptomes within their native context, they often lack single-cell resolution. Deconvolution methods can computationally infer tissue composition from spatial transcriptomics data, but differences in their workflows complicate their use and comparison. We developed spacedeconv, a unified interface to different deconvolution methods that additionally supports data preprocessing, visualization, and analysis of cell communication and multimodal data. Here, we demonstrate how spacedeconv streamlines the investigation of the cellular and molecular underpinnings of tissue architecture in different organisms and tissue contexts. Tissue architecture spatial transcriptomics cell-type deconvolution cellular composition next-generation sequencing data visualization. Full Text Additional Declarations Competing interest reported. Gregor Sturm is an employee of Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach, Germany. FF consults for iOnctura. Supplementary Files TableS1.xlsx TableS2.xlsx TableS3.xlsx TableS4.xlsx TableS5.xlsx TableS6.xlsx TableS7.xlsx TableS8.xlsx spacedeconvsupplfigures.pdf Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5102166","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":359834184,"identity":"8d6b05a8-4d84-4334-a171-cd3f9229fae8","order_by":0,"name":"Constantin Zackl","email":"","orcid":"","institution":"University of Innsbruck","correspondingAuthor":false,"prefix":"","firstName":"Constantin","middleName":"","lastName":"Zackl","suffix":""},{"id":359834185,"identity":"96a8ac06-43bb-434a-b1d4-5c34affa46e8","order_by":1,"name":"Maria Zopoglou","email":"","orcid":"","institution":"University of Innsbruck","correspondingAuthor":false,"prefix":"","firstName":"Maria","middleName":"","lastName":"Zopoglou","suffix":""},{"id":359834186,"identity":"54eba564-2560-41ac-9972-0f09d632f643","order_by":2,"name":"Reto Stauffer","email":"","orcid":"","institution":"University of Innsbruck","correspondingAuthor":false,"prefix":"","firstName":"Reto","middleName":"","lastName":"Stauffer","suffix":""},{"id":359834187,"identity":"7ee1952a-e8b4-460e-9d6e-ab9e2feb51bd","order_by":3,"name":"Markus Ausserhofer","email":"","orcid":"","institution":"University of Innsbruck","correspondingAuthor":false,"prefix":"","firstName":"Markus","middleName":"","lastName":"Ausserhofer","suffix":""},{"id":359834188,"identity":"5df2db77-2da1-4cea-9abd-06fb45363546","order_by":4,"name":"Marieke E. 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