Tutorials

In this section, you will find examples of how to use the bulkDGD package for different tasks.

If you want an overview of the command-line utilities available in bulkDGD, see the Command-line interface section.

Here, we will showcase the usage of the package’s functions in the context of larger analysis scripts.

Specifically, we provide detailed tutorials to:

• Find the best representations in latent space for a new set of samples (Tutorial 1).

• Perform differential expression analysis between a set of “treated” samples (for instance, cancer samples) and their corresponding “untreated” samples (“normal” samples) found using the bulkDGD model (Tutorial 2).

• Train the bulkDGD model on a new set of samples (Tutorial 3).

The data and Python scripts needed to reproduce the tutorials can be found in the different tutorial_* directories inside the bulkDGD/tutorials directory.