This repository contains slides and resources to accompany the DREAM Challenge webinars:

• Webinar 1 - Visual Interface

• Webinar 2 - Python and API

Documentation for the Seven Bridges Cancer Genomics Cloud (CGC) can be found at the CGC Knowledge Center.

dream_helpers.py is a library of helper functions to be used with the Python client of the Seven Bridges API. These functions are used in each notebook. It may be helpful to look through these functions to understand how API calls are made using the Python client.

Before using the notebooks below, you will want to do the following:

1. Copy the DREAM Challenge Project on the CGC visual interface.
2. Set up your API environment variables.
3. Change the IDs for username, project, ID, etc. in the notebooks to your own.

This walks through the SMC-RNA DREAM Challenge Public Project and includes instructions on how to submit tasks in which the smcIsoform-RSEM-workflow is run with DREAM Challenge training data. In addition, this notebook demonstrates how to evaluate the outputs of your workflow against truth sets.

This notebook describes how to run kallisto_quant.cgc.cwl to evaluate the accuracy of kallisto quant with training data.