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 1.0.0

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

Help Pages

.amplifyOneCell	This function simulates the amplification, library prep, and the sequencing processes.
.calAmpBias	Simulate technical biases
.continuousCIF	Generates cifs for cells sampled along the trajectory of cell development
.divideBatchesImpl	Divide the observed counts into multiple batches by adding batch effect to each batch
.expandToBinary	expand transcript counts to a vector of binaries of the same length of as the number of transcripts
.getCountCorrMatrix	This function finds the correlation between every pair of genes
.getParams	Get Kineic Parameters for all cells and genes
.normalizeGRNParams	Rename the original gene IDs in the GRN table to integers.
.rnormTrunc	sample from truncated normal distribution
.SpatialGrid	The class for spatial grids
add_expr_noise	Add experimental noise to true 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
gene_len_pool	a pool of gene lengths to sample from
gen_1branch	Generate true transcript counts for linear structure
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
len2nfrag	from transcript length to number of fragments (for the nonUMI protocol)
match_params	distribution of kinetic parameters learned from the Zeisel UMI cortex datasets
OP	Get option from an object in the current environment
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
SampleDen	sample from smoothed density function
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