UNAGI.UNAGI
- class UNAGI.UNAGI[source]
The UNAGI class is the main class of UNAGI. It contains the function to prepare the data, start the model training and start analysing the perturbation results.
Methods
__init__()analyse_UNAGI(data_path, iteration, ...[, ...])Perform downstream tasks including dynamic markers discoveries, hierarchical markers discoveries, pathway perturbations and compound perturbations.
calculate_neighbor_graph([neighbors, threads])The function to calculate the cell graphs for each stage.
register_CPO_parameters([anchor_neighbors, ...])The function to register the parameters for the CPO analysis.
register_iDREM_parameters([Normalize_data, ...])The function to register the parameters for the iDREM analysis.
register_species(species)The function to register the species of the single-cell data.
run_UNAGI(idrem_dir[, CPO, resume, ...])The function to launch the model training.
setup_data(data_path, stage_key, total_stage)The function to specify the data directory, the attribute name of the stage information and the total number of time stages of the time-series single-cell data.
setup_training(task, dist[, device, ...])Set up the training parameters and the model parameters.