Man pages for SRTsim
Simulator for Spatially Resolved Transcriptomics
| compareSRT | Summarize metrics for reference data and synthetic data |
| convert_grid | Convert continuous coordinate into integer, essential for... |
| 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... |
| 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... |
| 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... |
| srtsim_cci_ref | Generate Data with Cell-Cell Interaction Under... |
| srtsim_count | Generate Data with Estimated Parameters |
| srtsim_count_affine | Generate Data with Estimated Parameters For A New Designed... |
| 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... |
| visualize_metrics | Visualize summarized metrics for reference data and synthetic... |
