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.

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:

• configuration used to set up the bulkDGD model.

• configuration used to set the optimization scheme when finding representations for a new set of samples.

• configuration used to train the bulkDGD model.