ArticleGenome biology2023
SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 80 citations in OpenAlex.
- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- STADiffuser: high-fidelity simulation and full-view 3D modeling of spatial transcriptomics.Nature communications · 2026Article
- STGBench: sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic alterations.Briefings in bioinformatics · 2026Article
- Benchmarking sketching methods on spatial transcriptomics data.Nucleic acids research · 2026Article
- SpatialESD: Spatial Ensemble Domain Detection in Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Castl: robust identification of spatially variable genes in spatial transcriptomics via an ensemble-based framework.Briefings in bioinformatics · 2026Article
- BEASTsim-a benchmarking and analysis platform for spatial transcriptomics simulations.Briefings in bioinformatics · 2026Article
- Spider: a flexible and unified framework for simulating spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- DWGCN: distance-weighted graph convolutional network for robust spatial domain identification in spatial transcriptomics.Frontiers in genetics · 2026Article
- From features to slice: parameter-cloud modeling of spatial transcriptomics for simulation and 3D interpolatory augmentation.bioRxiv : the preprint server for biology · 2025Article
- Article
- Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.PLoS computational biology · 2025Article
- sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.Genome biology · 2025Article
- scSpatialSIM: a simulator of spatial single-cell molecular data.SoftwareX · 2025Article
- LSGI: interpretable spatial gradient analysis for spatial transcriptomics data.Genome biology · 2025Article
- Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.bioRxiv : the preprint server for biology · 2025Article
- Prioritizing perturbation-responsive gene patterns using interpretable deep learning.Nature communications · 2025Article
- SMOPCA: spatially aware dimension reduction integrating multi-omics improves the efficiency of spatial domain detection.Genome biology · 2025Article
- scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.Nature methods · 2025Article
- Benchmarking computational methods for detecting spatial domains and domain-specific spatially variable genes from spatial transcriptomics data.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.