Automatic Genomic Data Commons processing for bioinformaticians
Project description
# 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 . `
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