# Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions

## Documentation for package ‘scMultiSim’ version 1.2.0

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

## Help Pages

.SpatialGrid | The class for spatial grids
add_expr_noise | Add experimental noise to true counts
add_outliers | Add outliers to the observed counts
cci_cell_type_params | Generate cell-type level CCI parameters
dens_nonzero | this is the density function of log(x+1), where x is the non-zero values for ATAC-SEQ data
divide_batches | Divide batches for observed counts
gene_corr_cci | Plot the ligand-receptor correlation summary
gene_corr_regulator | Print the correlations between targets of each regulator
gen_clutter | generate a clutter of cells by growing from the center
Get_1region_ATAC_correlation | This function gets the average correlation rna seq counts and region effect on genes for genes which are only associated with 1 chromatin region
Get_ATAC_correlation | This function gets the average correlation rna seq counts and chromatin region effect on genes
GRN_params_100 | 100_gene_GRN is a matrix of GRN params consisting of 100 genes where: # - column 1 is the target gene ID, # - column 2 is the gene ID which acts as a transcription factor for the target (regulated) gene # - column 3 is the effect of the column 2 gene ID on the column 1 gene ID
GRN_params_1139 | GRN_params_1139 is a matrix of GRN params consisting of 1139 genes where: # - column 1 is the target gene ID, # - column 2 is the gene ID which acts as a transcription factor for the target (regulated) gene # - column 3 is the effect of the column 2 gene ID on the column 1 gene ID
Phyla1 | Creating a linear example tree
Phyla3 | Creating an example tree with 3 tips
Phyla5 | Creating an example tree with 5 tips
plot_cell_loc | Plot cell locations
plot_gene_module_cor_heatmap | Plot the gene module correlation heatmap
plot_grid | Plot the CCI grid
plot_grn | Plot the GRN network
plot_phyla | Plot a R phylogenic tree
plot_rna_velocity | Plot RNA velocity as arrows on tSNE plot
plot_tsne | Plot t-SNE visualization of a data matrix
run_shiny | Launch the Shiny App to configure the simulation
scmultisim_help | Show detailed documentations of scMultiSim's parameters
sim_example | Simulate a small example dataset with 200 cells and the 100-gene GRN
sim_example_spatial | Simulate a small example dataset with 200 cells and the 100-gene GRN, with CCI enabled
sim_true_counts | Simulate true scRNA and scATAC counts from the parameters
spatialGrid-class | The class for spatial grids
True2ObservedATAC | Simulate observed ATAC-seq matrix given technical noise and the true counts
True2ObservedCounts | Simulate observed count matrix given technical biases and the true counts