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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
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Add in MPNST PDX Data #146

Open sgosline opened 5 months ago

sgosline commented 5 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 4 months ago

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

sgosline commented 4 months ago

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

sgosline commented 4 months ago

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

sgosline commented 2 months ago

Requires creating a new drug processing script