SRTsim: Spatial Pattern Preserving Simulations for Spatially Resolved Transcriptomics

Authors

Jiaqiang Zhu
Lulu Shang
Xiang Zhou

Publication Date

3-3-2023

Journal

Genome Biology

Abstract

Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.

Keywords

Transcriptome, Gene Expression Profiling, Benchmarking, Cell Communication, Computer Simulation

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Associated Data

PMID: 36869394