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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
BSD 3-Clause "New" or "Revised" License
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consider adding PDX data #146

Open sgosline opened 2 months ago

sgosline commented 2 months ago

There is PDX data, though no RNASeq, availalbe from Orcestra.ca: https://www.orcestra.ca/xevaset/10.5281/zenodo.4302463

Is it useful to have pdx data that is not sequencing?

sgosline commented 1 month ago

Xeva schema is pretty basic, will work toward what PDXNet is doing.

sgosline commented 1 month ago

What tools are avaialble for processing? AFAIK its just XEVA but a more generic (or python-based) tool would be helpful

sgosline commented 1 month ago

Adding this: https://www.science.org/doi/full/10.1126/scitranslmed.abf4969 and this: https://codeocean.com/capsule/2817911/tree/v2