Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA).

ABSTRACT: Sequencing-based spatial transcriptomics (ST) methods allow unbiased capturing of RNA molecules at barcoded spots, charting the distribution and localization of cell types and transcripts across a tissue. While the coarse resolution of these techniques is considered a disadvantage, we argue that the inherent proximity of transcriptomes captured on spots can be leveraged to reconstruct cellular networks. To this end, we developed ISCHIA (Identifying Spatial Co-occurrence in Healthy and InflAmed tissues), a computational framework to analyze the spatial co-occurrence of cell types and transcript species within spots. Co-occurrence analysis is complementary to differential gene expression, as it does not depend on the abundance of a given cell type or on the transcript expression levels, but

SUBMITTER: Lafzi A 

PROVIDER: S-EPMC10897385 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature