search

ga4gh / fasp-scripts

Apache License 2.0
11 stars 7 forks source link

Access GTEX PFB data via Search #15

Closed ianfore closed 3 years ago

ianfore commented 3 years ago

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 commented 3 years ago

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,