SPROUT: spectral sparsification helps restore the spatial structure at single-cell resolution.

ABSTRACT: Single-cell RNA sequencing thoroughly quantifies the individual cell transcriptomes but renounces the spatial structure. Conversely, recently emerged spatial transcriptomics technologies capture the cellular spatial structure but skimp cell or gene resolutions. Ligand-receptor interactions reveal the potential of cell proximity since they are spatially constrained. Cell-cell affinity values estimated by ligand-receptor interaction can partially represent the structure of cells but falsely include the pseudo affinities between distant or indirectly interacting cells. Here, we develop a software package, SPROUT, to reconstruct the single-cell resolution spatial structure from the transcriptomics data through diminished pseudo ligand-receptor affinities. For spatial data, SPROUT first curates

SUBMITTER: Wang J 

PROVIDER: S-EPMC9477078 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature