Multi-task benchmarking of spatially resolved gene expression simulation models.

ABSTRACT:

Background

Computational methods for spatially resolved transcriptomics (SRT) are often developed and assessed using simulated data. The effectiveness of these evaluations relies on the ability of simulation methods to accurately reflect experimental data. However, a systematic evaluation framework for spatial simulators is currently lacking.

Results

Here, we present SpatialSimBench, a comprehensive evaluation framework that assesses 13 simulation methods using ten distinct STR datasets. We introduce simAdaptor, a tool that extends single-cell simulators by incorporating spatial variables, enabling them to simulate spatial data. SimAdaptor ensures SpatialSimBench is backwards compatible, facilitating direct comparisons between spatially aware simulators and existing non-spat

SUBMITTER: Liang X 

PROVIDER: S-EPMC11912772 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature