GdcAnalysis

Tools for analysing NIH GDC data

To get started

On the commandline, clone the repo from GitHub:

git clone https://github.com/awr01/GdcAnalysis.git

On the commandline, set up python:

pip install tqdm requests numpy scipy openpyxl

Download the raw NIH GDC dataset:

python GdcDownload.py --dest NIH_GDC_dataset.tar

where the NIH_GDC_dataset.tar can be any valid filename. This will take ~4 hours, download ~18GB of raw data and produce a 9GB output file.

The downloader keeps a cache in the .cache folder in case it is interrupted. If an error occurs on a cached operation, you can try deleting the cached file being used, or failing that, the entire .cache folder.

Once the file is successfully downloaded, the .cache folder can be deleted to free 18GB of disk space.

Run the various analysis tools

python Gdc.py --src [SOURCE FILE] 
              --dest [OUTPUT FILE] 
              --output [ANALYSIS TYPE] 
              --classification [DATA CLASSIFICATION]

• [SOURCE FILE] - The tar file containing the dataset
• [OUTPUT FILE] - Optional. Explicitly specify output file name, otherwise a default file name is defined from the other flags.
• [ANALYSIS TYPE] - Specify the analysis output type. Three options:
  • Volcano - Volcano plots (p-value vs. fold-ratio) of star-counts for all available genes for ATRX Mutant vs. Wildtype, for each classification
  • BoxPlot - Box plots of DRG2 star-counts for ATRX Mutant vs. Wildtype, for each classification
  • Excel - Microsoft Excel spreadsheet, with one sheet per classification, each giving the star-count statistics for all available genes for ATRX Mutant vs. Wildtype
• [DATA CLASSIFICATION] - How the data is classified for analysis
  • PerDisease - Classify the data according to NIH GDC diagnosis label
  • BroadClasses - Classify the NIH GDC diagnosis label more broadly as "Carcinoma", "Melanoma", "Leukemia", "None", "Unspecified" and "Other"

Examples:

python Gdc.py --src NIH_GDC_dataset.tar --output BoxPlot --classification PerDisease
python Gdc.py --src NIH_GDC_dataset.tar --output BoxPlot --classification BroadClasses
python Gdc.py --src NIH_GDC_dataset.tar --output Volcano --classification PerDisease
python Gdc.py --src NIH_GDC_dataset.tar --output Volcano --classification BroadClasses
python Gdc.py --src NIH_GDC_dataset.tar --output Excel   --classification PerDisease
python Gdc.py --src NIH_GDC_dataset.tar --output Excel   --classification BroadClasses