Simulator for Spatially Resolved Transcriptomics
Summarize gene-wise summary metrics
Summarize location-wise summary metrics
Access User-Specified Parameters
Access reference colData
Access reference count matrix
Access reference rowData
ReSimulate Count Data with Parameters Specification from Shiny
Create a SRTsim object from reference-free shinyoutput
Access synthetic colData
Access synthetic count matrix
Fit the marginal distributions for single gene
Access synthetic rowData
Summarize metrics for reference data and synthetic data
Convert continuous coordinate into integer, essential for BayesSpace t...
Create simSRT object
Access Model Fitting Parameters
fitting data with poisson through optim function
Extracted summarized metrics for reference data and synthetic data
Generate Data with Cell-Cell Interaction Under Reference-Free Mode
Generate Data with Cell-Cell Interaction Under Reference-Based Mode
Generate Data with Estimated Parameters For A New Designed Pattern
Generate Data with Estimated Parameters
Fit the marginal distributions for each row of a count matrix
Fit the marginal distributions for each row of a count matrix
Run the SRTsim Shiny Application
Subset SRT object based on domain labels of interest
Visualize expression pattern for the gene of interest in reference dat...
Visualize summarized metrics for reference data and synthetic data
An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.