CellSP enables module discovery and visualization for subcellular spatial transcriptomics data.

ABSTRACT: Spatial transcriptomics has enabled the study of mRNA distributions within cells, a key aspect of cellular function. However, there is a dearth of tools that can identify and interpret functionally relevant spatial patterns of subcellular transcript distribution. To address this, we present CellSP, a computational framework for identifying, visualizing, and characterizing consistent subcellular spatial patterns of mRNA. CellSP introduces the concept of "gene-cell modules", which are gene sets with coordinated subcellular transcript distributions in many cells. It provides intuitive visualizations of the captured patterns and offers functional insights into each discovered module. We demonstrate that CellSP reliably identifies functionally significant modules across diverse tissues and tech

SUBMITTER: Aggarwal B 

PROVIDER: S-EPMC12589652 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature