.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 |