TCGA COAD and READ annotations missing from GDC commons?
1 answer
Some alternatives:
- GDAC Firehose (all pre-2016 TCGA data): http://gdac.broadinstitute.org/runs/stddata__latest/
- ICGC Data Portal (includes some TCGA data): https://dcc.icgc.org/
For some reason, some of the data didn't port over to GDC from the old TCGA portal.
I had a similar question earlier: Why is TCGA Genomic Data Commons missing some data?
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Such annotation still exist in GDC as "annotation" nodes in the GDC Database, and queryable using APIs. As all metadata in GDC are maintained in a single Graph Database and accessible by API (and UI), there are no separate "annotation database" or "annotation manager" in GDC.