Repository files navigation

This is a mixed notebook and data repository for retrieving cancer data forProject Cognoma.Currently, all data is from theTCGA Pan-Cancer collection of the UCSC Xena Browser.

The data acquisition and analysis is executing by running Jupyter notebooks in the following order:

• 1.TCGA-download.ipynb — download and compress TCGA datasets.
• 2.TCGA-process.ipynb — convert downloaded TCGA datasets into sample × gene matrixes.

Theexecute.sh script executes the notebooks in order.After installing and activating theenvironment, run with the commandbash execute.sh from the repository's root directory.

The repository contains the following directories:

• download — contains files retrieved from an external location whose content is unmodified.Large downloaded files are tracked using Git LFS.Associated metadata files are also retained for versioning.
• data — contains generated datasets.The complete matrix files are not currently tracked due to file size, but randomly-subsetted versions are available for development use (seedata/subset).

The complete datasets created by this repository (data/expression-matrix.tsv.bz2 anddata/mutation-matrix.tsv.bz2) are uploaded tofigshare.Since this is a manual process, check the figshare REFERENCES section to see which commit these datasets derive from.In other words, the latest version on figshare may lag behind this repository.

This repository usesconda to manage its environment, which is namedcognoma-cancer-data.The required packages and versions are listed inenvironment.yml.If as a developer, you require an additional package, add it toenvironment.yml.

The following commands install and activate the environment:

# Create or overwrite the cognoma-cancer-data conda environmentconda env create --file=environment.yml# Activate the conda environment (assumes conda >= 4.4)conda activate cognoma-cancer-data

This repository is dual licensed asBSD 3-Clause andCC0 1.0, meaning any repository content can be used under either license.This licensing arrangement ensures source code is available under anOSI-approved License, while non-code content — such as figures, data, and documentation — is maximally reusable under a public domain dedication.