# Simulator for Spatially Resolved Transcriptomics

## Documentation for package ‘SRTsim’ version 0.99.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

compareSRT | Summarize metrics for reference data and synthetic data
convert_grid | Convert continuous coordinate into integer, essential for BayesSpace to determine the neighborhood info
createSRT | Create simSRT object
EstParam | Access Model Fitting Parameters
exampleLIBD | Data used for creating vignettes
fit_pos_optim | fitting data with poisson through optim function
get_metrics_pd | Extracted summarized metrics for reference data and synthetic data
get_stats_gene | Summarize gene-wise summary metrics
get_stats_loc | Summarize location-wise summary metrics
metaParam | Access User-Specified Parameters
refcolData | Access reference colData
refCounts | Access reference count matrix
refrowData | Access reference rowData
reGenCountshiny | ReSimulate Count Data with Parameters Specification from Shiny
Shiny2SRT | Create a SRTsim object from reference-free shinyoutput
simcolData | Access synthetic colData
simCounts | Access synthetic count matrix
simNewLocs | Fit the marginal distributions for single gene
simrowData | Access synthetic rowData
srtsim_cci_free | Generate Data with Cell-Cell Interaction Under Reference-Free Mode
srtsim_cci_ref | Generate Data with Cell-Cell Interaction Under Reference-Based Mode
srtsim_count | Generate Data with Estimated Parameters
srtsim_count_affine | Generate Data with Estimated Parameters For A New Designed Pattern
srtsim_fit | Fit the marginal distributions for each row of a count matrix
srtsim_newlocs | Fit the marginal distributions for each row of a count matrix
SRTsim_shiny | Run the SRTsim Shiny Application
subsetSRT | Subset SRT object based on domain labels of interest
toyData | A toyExample to showcase reference-based simulations
toyShiny | A toyExample to showcase reference-free simulations
visualize_gene | Visualize expression pattern for the gene of interest in reference data and synthetic data
visualize_metrics | Visualize summarized metrics for reference data and synthetic data