Metadata-Version: 2.1
Name: autoGDC
Version: 0.0.1
Summary: Automatic Genomic Data Commons processing for bioinformaticians
Home-page: https://gitlab.com/chase_brown/autogdc
Author: Chase Brown
Author-email: chase.brown.2016@gmail.com
License: UNKNOWN
Keywords: bioinformatics meta-analysis GDC Genomic-Data-Commons data-repository
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Requires-Dist: wrenlab
Requires-Dist: pandas
Requires-Dist: cruzdb @ git+git://github.com/brentp/cruzdb.git@pull16
Requires-Dist: oursql3 @ git+git://github.com/sqlobject/oursql.git@py3k
Requires-Dist: rpy2

# autoGDC

![logo](https://raw.githubusercontent.com/chasealanbrown/autoGDC/master/autoGDC_logo.png)

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 .
```


