tcga-blca

Example using Cohorts to manage TCGA-BLCA for analysis

1. Query GDC for clinical and sample datasets for TCGA-BLCA data (query code to be merged into pygdc)
2. Set up a Cohort using Cohorts to manage these data
3. Mock-analysis of said Cohort to show functionality of Cohorts.

Setup

There are a few steps you will have to follow before using this code.

• Copy config_template.ini to config.ini
• Install gdc-client.
  • Install per the instructions
  • Edit the variable GDC_CLIENT_PATH in config.ini
• Log into GDC, request access to TCGA & download an auth-token
  1. Gain authorization
  2. Download the authentication token
  3. Edit the variable GDC_TOKEN_PATH in config.ini

Once you have these items set up, you can run one or both of the refresh_*.py scripts to fetch data from the GDC portal.

Then, you can try out the various *.ipynbs in the repo for yourself, or use them as a starting point for further analysis.

query_tcga

The refresh_*.py scripts make use of the query_tcga package. This cannot currently be installed via pip.

Instead, you will want to install as follows:

pip install git+git://github.com/jburos/query_tcga

This code will eventually be merged into the cleaner pygdc package. For now, the merge of these codebases is a WIP.