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April 14th, 2025
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Institute of Clinical Medicine, Department of Pathology, Oslo University Hospital
bioinformatics
biorxiv

Easydecon: A Lightweight Workflow for Cell Type Analysis in High-Definition Spatial Transcriptomics Assays

Umu, S. U.Open in Google Scholar•Karlsen, V. T.Open in Google Scholar•Baekkevold, E. S.Open in Google Scholar•Jahnsen, F. L.Open in Google Scholar•Domanska, D.Open in Google Scholar

Spatial transcriptomics enables mapping gene expression within tissue structures. VisiumHD by 10x Genomics advances this further, offering near-single-cell resolution across tissue sections. Here we introduce Easydecon, a lightweight bioinformatics workflow leveraging similarity algorithms and regression-based cell type proportion estimation to transfer cell types and deconvolute spatial bins. Easydecon streamlines visualization and spatial deconvolution by utilizing differentially expressed genes identified from single-cell RNA sequencing datasets.

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