CRI-iAtlas / shiny-iatlas

An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
https://www.cri-iatlas.org
Apache License 2.0
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Identify any non-feature matrix data that needs to be loaded #4

Closed jaeddy closed 6 years ago

jaeddy commented 6 years ago

Some data (e.g., immunomodulator gene annotations) won't be stored in the IRWG feature matrix. Need to enumerate these datasets and make sure they're available to the Shiny app.

vthorsson commented 6 years ago
  1. Manifest file for Feature Variables - work already well under way
  2. Immunomodulator list, and annotations can be found at https://docs.google.com/spreadsheets/d/1aqOXYsU1ubkbxIZI_5p8ZRootgOAT0KweMA3LvSZ7HY/edit?usp=sharing
  3. Per-gene , per-sample values for gene expression , DNA methylation, and Copy Number can be found on BigQuery Pancancer Atlas mirror. For example gene expression values are https://bigquery.cloud.google.com/table/isb-cgc-01-0008:Filtered.EBpp_AdjustPANCAN_RNASeqV2_filtered
andrewelamb commented 6 years ago

immunomodulator data is now being loaded from google sheets

andrewelamb commented 6 years ago

immunomodulator gene expression data was pulled form bq. I saved this as a tsv in the repo to be used locally, but the function pull form bq was saved for future use.