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Updates to the NF-OSI study #1760

Merged
merged 26 commits into from
Feb 1, 2023
Merged

Updates to the NF-OSI study #1760

merged 26 commits into from
Feb 1, 2023

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rmadupuri
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@rmadupuri rmadupuri commented Jan 31, 2023 •
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Data is from #1736 submitted by @anngvu and @jaybee84.

The following additional changes were made on files:

  • Updates study ID to nst_nfosi_2022
  • Annotated the MAF using Genome Nexus - https://grch38.genomenexus.org/
  • Fixed clinical data to cBioPortal standards
  • Added TMB Scores

anngvu and others added 24 commits November 9, 2022 10:55
@anngvu
Add mixed_nfosi_2022
1b06d33
@anngvu
Update citation
80eda99
@anngvu
Add LICENSE
a51692c
@anngvu
Update meta
363e23f
@anngvu
Fix cell line sample file manually
b6b8b42
@anngvu
Generate case lists
e23dc9d
@anngvu
Update name
635cd21
@anngvu
Update validation html report
438ee64
@anngvu
Use v3 of mutations data
e811deb
@anngvu
Update validation result
914ea35
@anngvu
Merge branch 'cBioPortal:master' into newstudy/nfosi_2022
3cdb88c
@anngvu
Replace bioRxiv citation with better citation
2f8ea47
@anngvu
Update study name per review suggestion
d8ad6a4
@anngvu
Use cleaner citation format per review suggestion
bf74461
@anngvu
Add pmid field to study meta per review suggestion
43c6ca0
@anngvu
Add reference_genome field per review suggestion
51e8efe
@anngvu
Recategorize type_of_cancer per review suggestion
cc7f48e
@anngvu
Rename files, no longer use _extended suffix
660fd5d
@anngvu
Rename all case list file to cases_all.txt per review suggestion
b498f94
@anngvu
Use nst in study id per suggestion
97184bf
@anngvu
Whoops, propagate study id changes to case list files
d929f69
@rmadupuri
Merge branch 'newstudy/nfosi_2022' of https://github.com/nf-osi/datahub…
10b8db9 
… into nfosi_study
@rmadupuri
update study name, fix clinical, meta data
caf90e0
@rmadupuri
remove html report
a245ecb
@rmadupuri rmadupuri mentioned this pull request Jan 31, 2023
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@sbabyanusha sbabyanusha merged commit aba0099 into master Feb 1, 2023
@rmadupuri rmadupuri deleted the nfosi_study branch February 9, 2023 15:50
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@sbabyanusha sbabyanusha sbabyanusha approved these changes

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3 participants
@rmadupuri @sbabyanusha @anngvu