TY - JOUR
T1 - SRTsim
T2 - spatial pattern preserving simulations for spatially resolved transcriptomics
AU - Zhu, Jiaqiang
AU - Shang, Lulu
AU - Zhou, Xiang
N1 - Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85149543371&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85149543371&partnerID=8YFLogxK
U2 - 10.1186/s13059-023-02879-z
DO - 10.1186/s13059-023-02879-z
M3 - Article
C2 - 36869394
AN - SCOPUS:85149543371
SN - 1474-7596
VL - 24
JO - Genome biology
JF - Genome biology
IS - 1
M1 - 39
ER -