scAdam

Module for cell type annotation using downloaded or custom scAdam model.

Cross-tissue fast multi-level multi-class cell type annotation.

Download model

Download pretrained model from scParadise repository.

scadam.available_models	Download dataframe with available pretrained scAdam models.
scadam.download_model	Download pretrained tuned model for highly accurate cell type annotation.

Model training and optimization

Train custom scAdam model using your own reference dataset. Warm start training and hyperparameter tuning are also available to achieve better model performance.

scadam.train	Train custom scAdam model using annotated data matrix (adata).
scadam.warm_start	Warm-start training of scAdam model.
scadam.hyperparameter_tuning	Hyperparameter tuning using the automatic model optimization framework Optuna.
scadam.train_tuned	Train the scAdam model using parameters tuned by the 'scparadise.scadam.hyperparameter_tuning' function.

Prediction

Cell type annotation using downloaded or custom scAdam model.

scadam.predict

Predict cell types and cell type probilities using pretrained scAdam model.