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Gdcdocs #1918

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averyniceday
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@averyniceday averyniceday commented Sep 20, 2023 •
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Add documentation for NCI-CRDC pipeline studies

Cancer studies updated in this pull request:
None - but will reference _gdc studies

checks

For all pull requests:

  • Passes validation

For a new study (in addition to above):

  • Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
  • is study meta data complete? e.g. pmid, group of PUBLIC
  • were all samples profiled with WES/WGS? If not, is gene panel file curated?
  • are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
  • clinical sample and patient data with meta files
  • mutations data with meta files
  • MAF is based on hg19
  • MAF with 2 isoforms: uniprot and mskcc
  • CNA data with meta files
  • CNA segment data with meta files
  • Expression data including z-scores with meta files
  • Case-lists for all profiles.
  • Manual checking (Niki or JJ): Triage or private Portal link here

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3 participants
@averyniceday @jamesqo @rmadupuri