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NIH-NCPI / FHIR-CAT-June22

Technical interop pilot using RNASeq data
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Adds case study notebooks #17

Closed bwalsh closed 2 years ago

bwalsh commented 2 years ago

This PR adds notebooks exploring data.

The case_studies/case-study-gtex_v8.ipynb is the most complete. It created the data frame that complies with the specification in #11 The dataframe is available at gs://fc-be286b9f-3acf-4168-af6e-592df509391d/gtex_v8-dataframe.tsv

The KidsFirst notebooks were not refined today. If desired they could be made compliant by merging the dataframes they do create, ensuring column names and exporting to tsv as was done for gtex.

All these data frames are available in the https://anvil.terra.bio/#workspaces/ncpi-fhir-2022/NCPI%20FHIR%20CAT%202022%20-%20Working%20Space workspace.

The gtex source data is here: fc-be286b9f-3acf-4168-af6e-592df509391d/gtex_v8

The KF data is here: fc-be286b9f-3acf-4168-af6e-592df509391d/kids_first

bwalsh commented 2 years ago

Anything we need to do to merge this PR?