Simulator for Spatially Resolved Transcriptomics

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Documentation for package ‘SRTsim’ version 0.99.7

• 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