API reference#

bulkdgd consists of several packages:

  • analysis, containing utilities to analyze the data produced by the bulkdgd model.

  • core, containing the core components of the bulkdgd model and the model itself.

  • genes, containing utilities to create customized lists of genes to use with the bulkdgd model.

  • ioutil, containing utilities for loading and saving files and pre-process data.

  • plotting, containing plotting utilities.

  • recount3, containing utilities to interact with the Recount3 platform.

  • reproducibility, containing bulkdgd.reproducibility.set_seeds(), which seeds the generators a run draws from. It has to be called before the model is built, since building it already draws the decoder’s weights.

Some functions and methods use dictionary-based configurations for several tasks, such as setting up the bulkdgd model, finding the best representations for a new set of samples and training the bulkdgd model. More detailed descriptions of such configurations are available here: