Add an end to end workflow example

[csmagnano]

This would involve pathway creation over a range of hyperparameters. It would be useful for users understanding how to use PPA in a full analysis.

[agitter]

While testing Omics Integrator 2 for this parameter advising pipeline, @emmagraham found that it has built-in support for a parameter grid search. See the exampe notebook OI2_pipeline.ipynb. However, she had to make a slight modification to the code to output the networks for each parameter combination.

This makes Omics Integrator 2 appealing for our end-to-end workflow example. The overall workflow would be something like:

• Install Omics Integrator 2 through conda
• Install PGD and pathway parameter advising using the setup script
• Run Omics Integrator 2 parameter sweep
• Run pathway parameter advising on the predicted pathways
• Report or visualize the results