AutoGDC: A Python Package for DNA Methylation and Transcription Meta-Analyses
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Motivation
The Genomic Data Commons is a powerful resource which facilitates the exploration of molecular alterations across various diseases. However, utilizing this resource for meta-analysis requires many different tools to query, download, organize, and analyze the data. In order to facilitate a more rapid, simple means of analyzing DNA methylation and RNA sequencing datasets from the GDC we developed autogdc , a python package that integrates data curation and preprocessing with meta-analysis functionality into one simplified bioinformatic pipeline.
Availability and Implementation
The autogdc python package is available under the GPLv3 license at along with several examples of typical use-case scenarios in the form of a jupyter notebook. The data is all originally provided by the GDC, and is therefore available under the NIH Genomic Data Sharing (GDS) and NCI GDS policies.
