Name: tcga-blca
Owner: Hammer Lab
Description: Example analysis using Cohorts & TCGA-BLCA data
Created: 2016-09-13 04:15:14.0
Updated: 2016-09-27 20:46:38.0
Pushed: 2016-09-27 20:41:10.0
Size: 763
Language: Jupyter Notebook
GitHub Committers
User | Most Recent Commit | # Commits |
---|---|---|
Jacki Buros Novik | 2016-09-27 20:41:05.0 | 82 |
Other Committers
User | Most Recent Commit | # Commits |
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Example using Cohorts to manage TCGA-BLCA for analysis
There are a few steps you will have to follow before using this code.
config_template.ini
to config.ini
GDC_CLIENT_PATH
in config.ini
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.
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.