Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information.

ABSTRACT:

Background

Cell-cell interactions are important for information exchange between different cells, which are the fundamental basis of many biological processes. Recent advances in single-cell RNA sequencing (scRNA-seq) enable the characterization of cell-cell interactions using computational methods. However, it is hard to evaluate these methods since no ground truth is provided. Spatial transcriptomics (ST) data profiles the relative position of different cells. We propose that the spatial distance suggests the interaction tendency of different cell types, thus could be used for evaluating cell-cell interaction tools.

Results

We benchmark 16 cell-cell interaction methods by integrating scRNA-seq with ST data. We characterize cell-cell interactions into short-range and long-r

SUBMITTER: Liu Z 

PROVIDER: S-EPMC9575221 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature