API

The API reference contains detailed descriptions of the different end-user classes, functions, methods, etc.

Note

This API reference only contains end-user documentation. If you are looking to hack away at scArches’ internals, you will find more detailed comments in the source code.

Import scarches as:

import scarches as sca

After reading the data (sca.data.read), you can you can instantiate one of the implemented models from sca.models module (currently we support trVAE, scVI, scANVI, and TotalVI) and train it on your dataset.

• Data Processing
  • label_encoder()
  • remove_sparsity()
  • trVAEDataset
• Models
  • trVAE
  • expiMap
  • scPoli
  • scVI
  • scANVI
  • TotalVI
• Plotting
  • SCVI_EVAL
  • TRVAE_EVAL
  • plot_abs_bfs()
  • sankey_diagram()
• Utils
  • add_annotations()
  • weighted_knn_trainer()
  • weighted_knn_transfer()
• Zenodo
  • download_model()
  • upload_model()
  • Deposition helpers
  • File Helpers