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https://github.com/cumbof/opengdc.py

Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC

https://github.com/cumbof/opengdc.py

Science Score: 39.0%

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (4.3%) to scientific vocabulary

Keywords

bed bioinformatics cancer gdc metadata tcga
Last synced: 5 months ago · JSON representation

Repository

Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC

Basic Info
  • Host: GitHub
  • Owner: cumbof
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 94.9 MB
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bed bioinformatics cancer gdc metadata tcga
Created over 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

OpenGDC.py

This is the Python implementation of the original OpenGDC Java software https://github.com/cumbof/OpenGDC

Usage

``` python OpenGDC.py [--tumor [GDCTUMOR] ] [--datatype [GDCDATATYPE] ] [--after [AFTERDATETIME] ] [--download [DOWNLOADFLAG] ] [--downloaddir [DOWNLOADDIRECTORY] ] [--convert [CONVERTFLAG] ] [--convertdir [CONVERTDIRECTORY] ] [--matrix [EXPORTTOMATRIX] ] [--settings [SETTINGSFILE] ] [--verbose [VERBOSE_FLAG] ]

Optional arguments: --after [AFTERDATETIME] --matrix [EXPORTTO_MATRIX]

Notes: - both --tumor and --datatype are case sensitive; - flags --download and --convert activate the download and conversion of the GDC data; - at least one flag between --download and --convert must be specified; - the convertion procedure requires both the --download_dir and --convert-dir, additionally to the --convert flag enabled.

WARNING: --matrix still must be implemented --datatype supports only - "Methylation Beta Value" - "Clinical and Biospecimen Supplements" ```

Credits

Please credit our work in your manuscript by citing:

Eleonora Cappelli, Fabio Cumbo, Anna Bernasconi, Arif Canakoglu, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek. "OpenGDC: unifying, modeling, integrating cancer genomic data and clinical metadata" Appl. Sci. 2020, 10(18), 6367. https://doi.org/10.3390/app10186367

Owner

  • Name: Fabio Cumbo
  • Login: cumbof
  • Kind: user
  • Location: Cleveland, OH, USA
  • Company: Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Ph.D. in Computer Science and Automation Engineering, Postdoctoral Research Fellow @BlankenbergLab, GMI, LRI, Cleveland Clinic, USA

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