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

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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