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Access GTEX PFB data via Search #15

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ianfore opened this issue Jan 18, 2021 · 1 comment
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Access GTEX PFB data via Search #15

ianfore opened this issue Jan 18, 2021 · 1 comment
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FASPHackathon2 January 2021 FASP Hackathon

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@ianfore
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ianfore commented Jan 18, 2021 •
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Relevant to #14 more detailed search of GTEx subject and specimen (phenotypic) data is possible via data which may be exported from Anvil.

Obtaining GTEx subject and specimen data in this way is described here.

A user might load these data to a private BigQuery tables. A pull request has been submitted to pypfb which supports this.

Such tables could be incorporated into a FASP workflow using BigQuerySearchClient.

Alternatively a private GA4GH Server could be set up to access these data.
@ianfore ianfore added the FASPHackathon2 January 2021 FASP Hackathon label Jan 18, 2021
@ianfore ianfore mentioned this issue Jan 18, 2021
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ianfore commented Mar 1, 2021

Pypfb code generated BigQuery tables created.

Notebook to search these tables via BigQuery API created. As the GTEx data are controlled access am stopping short of moving them in to the public Search implementation. Waiting on controlled access Search,

@ianfore ianfore closed this as completed Mar 1, 2021
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