Reference-free single-cell-resolution deconvolution of spot-based spatial transcriptomics with CoexpressDeconvolve (STAR Protocols)

Spot-based spatial transcriptomics captures whole-transcriptome signal per spot but mixes multiple cells. This protocol describes CoexpressDeconvolve1 a reference-free approach that reconstructs single-cell-resolution, whole-transcriptome profiles directly from 10x Visium spots. We detail housekeeping-gene cell-density calibration, joint overdispersed-gene selection, a gene co-expression manifold, topic-number selection, consensus latent Dirichlet allocation, and hierarchical Bayesian sampling, then export to a 10x-compatible object for standard single-cell and spatial cell-cell communication analysis.