autoGDC

This package was created for automatic downloading and processing of Genomic Data Commons data.

Why?

The GDC is a great resource; however the process of downloading the data and combining it into a simple format can be time consuming. This package makes this more streamlined.

Examples of a few questions that may be explored are provided:

1. *DNA Methylation Clock*: What sites are chosen when training a DNA methylation clock model? How do they differ when different techniques are applied to retreive these sites?
2. *RNA vs. DNA methylation*: What is the correlation between transcription and DNAm for paired data?
3. *DNA methylation sequence modeling*: How much information is contained within sequence information of DNA methylation with respect to transcription?
4. *Glioblastoma Differential Gene Expression*: What is the DEG signature for glioblastoma patients?

These examples can help provide as a basis for how to use this package effectively.

Installation

The package autoGDC is available on pypi:

pip install autoGDC

Installation from source

git clone https://github.com/chasealanbrown/autoGDC
cd autoGDC

followed by either:

python setup.py install

or for development mode installation

python -m pip install -e .