API

Import scDesign3Py as:

import scDesign3Py

scDesign3

`scDesign3`([n_cores, parallelization, ...])	Python interface for scDesign3
`scDesign3.__init__`([n_cores, ...])	Decide basic settings when running the class methods.
`scDesign3.construct_data`(anndata, corr_formula)	Construct the input data
`scDesign3.fit_marginal`(mu_formula, ...[, ...])	Fit the marginal models
`scDesign3.fit_copula`([input_data, copula, ...])	Fit the copula model
`scDesign3.extract_para`([data, ...])	Extract the parameters of each cell's distribution
`scDesign3.simu_new`([mean_mat, sigma_mat, ...])	Simulate new data
`scDesign3.scdesign3`(anndata, corr_formula, ...)	The wrapper for the whole scDesign3 pipeline
`scDesign3.set_r_random_seed`(seed)	Set the R random seed

`get_bpparam`([mode, show])	Get your parallelization parameters robject
`perform_lrt`(alter_marginal, null_marginal)	Perform the likelihood ratio test
`plot_reduceddim`(ref_anndata, anndata_list, ...)	Dimensionality reduction and visualization