autoGDC 0.0.1

Automatic Genomic Data Commons processing for bioinformaticians

# 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:

• 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?</li>

• RNA vs. DNA methylation: What is the correlation between transcription and DNAm for paired data?</li>

• DNA methylation sequence modeling: How much information is contained within sequence information of DNA methylation with respect to transcription?</li>

• Glioblastoma Differential Gene Expression: What is the DEG signature for glioblastoma patients?</li>

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

## Installation The package autoGDC is available on pypi:

`sh pip install autoGDC `

## Installation from source

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

followed by either:

`sh python setup.py install `

or for development mode installation

`sh python -m pip install -e . `