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Add cBioPortal/TCGA processor #8

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bgyori opened this issue May 9, 2021 · 2 comments
Open

Add cBioPortal/TCGA processor #8

bgyori opened this issue May 9, 2021 · 2 comments
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Processor A new processor

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@bgyori
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bgyori commented May 9, 2021

One approach is to process the raw data into summary statistics of interest. For instance, define a list of disease types and pool all the studies for that particular disease. Then calculate the mutation frequency of genes appearing across all studies for that disease, and create gene-mutated_in (frequency: x%)->disease relations to capture the data.

@bgyori bgyori added the Processor A new processor label May 9, 2021
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bgyori commented May 9, 2021

cBioPortal also contains the CCLE cell line data set which could be used to add expression relations between genes and cell lines, see e.g., https://github.com/sorgerlab/indra/blob/master/indra/databases/context_client.py.

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bgyori commented Sep 14, 2021

Parts of this were done in #32 but the original idea is not yet integrated.

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