Simulating Spatial Cell-Cell Interactions | Speeding up the Simulation | Spatial layouts | Built-in layouts | Custom layouts | Spatial domains | Spatially variable genes | Long-distance Cell-Cell Interactions | Session Information

Installation | Running Simulation | The Shiny app | Add technical noise and batch effect | Visualize the results

Simulating True Counts | GRN and Differentiation Tree | Omitting the GRN | Running the Simulation | Accessing the Results | Visualizing the Results | Adding Technical Variation and Batch Effect | Adding technical noise | Adding batch effects | Adjusting Parameters | The Shiny App | Deciding Number of CIFs: num.cifs | Discrete Cell Population: discrete.cif | Adjusting the Effect of Cell Population: diff.cif.fraction | Adjusting the Inherent Cell Heterogeneity: cif.mean and cif.sigma | Adjusting the Intrinsic Noise: intinsic.noise | Adjust the effect of chromatin accessibility: atac.effect | Simulating Dynamic GRN | Session Information

Options: General | rand.seed | threads | speed.up | Options: Genes | GRN | num.genes | unregulated.gene.ratio | giv.mean, giv.sd, giv.prob | dynamic.GRN | hge.prop, hge.mean, hge.sd | hge.range | hge.max.var | Options: Cells | num.cells | tree | discrete.cif | discrete.min.pop.size, discrete.min.pop.index | discrete.pop.size | Options: CIF | num.cifs | diff.cif.fraction | cif.center, cif.sigma | use.impulse | Options: Simulation - ATAC | atac.effect | region.distrib | atac.p_zero | riv.mean, riv.sd, riv.prob | Customization | mod.cif.giv | ext.cif.giv | Optins: Simulation | vary | bimod | scale.s | intrinsic.noise | Options: Simulation - RNA Velocity | do.velocity | beta | d | num.cycles | cycle.len | Options: Simulation - Spatial Cell-Cell Interaction | grid.size | layout | step.size | params | cell.type.interaction | cell.type.lr.pairs | max.neighbors | radius | start.layer