# A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

## Documentation for package ‘scDesign3’ version 1.8.0

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

## Help Pages

ba | Functions from gamlss/gamlss.add with bugs fixed
construct_data | Construct the input data (covariate matrix and expression matrix)
example_count | A sparse matrix with example data
example_sce | A SingleCellExperiment object containing both cell type and pseudotime
extract_para | Extract the parameters of each cell's distribution
fit_copula | Fit the copula model
fit_marginal | Fit the marginal models
ga | Functions from gamlss/gamlss.add with bugs fixed
gamlss.ba | Support for Function ba()
gamlss.ga | Support for Function ga()
perform_lrt | Perform the likelihood ratio test
plot_reduceddim | Dimensionality reduction and visualization
pseudotime | A numeric vector of pseudotime values
scdesign3 | The wrapper for the whole scDesign3 pipeline
simu_new | Simulate new data
sparse_cov | This function computes the thresholding sparse covariance/correlation estimator with the optimal threshold level.