GwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics.

ABSTRACT: Most spatial transcriptomics (ST) technologies (e.g. 10× Visium) operate at the multicellular level, where each spatial location often contains a mixture of cells with heterogeneous cell types. Thus, effective deconvolution of cell type compositions is critical for downstream analysis. Although reference-based deconvolution methods have been proposed, they depend on the availability of reference data, which may not always be accessible. Additionally, within a deconvolved cell type, cellular heterogeneity may still exist, requiring further deconvolution to uncover finer structures for a better understanding of this complexity. Here, we present gwSPADE, a gene frequency-weighted reference-free SPAtial DEconvolution method for ST data. gwSPADE requires only the gene count matrix and utilizes

SUBMITTER: Xie A 

PROVIDER: S-EPMC12464827 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature