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v12 release notes #352

Merged
merged 5 commits into from
Apr 30, 2023
Merged

v12 release notes #352

merged 5 commits into from
Apr 30, 2023

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kelseykeith
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Purpose/implementation Section

What scientific question is your analysis addressing?

Updated the release notes for v12

What was your approach?

Added changes for v12, particularly additional files and the update to GENCODE v39

What GitHub issue does your pull request address?

Ticket 463

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Release notes were primarily written using the tickets linked in v12 release ticket Ticket 431, however, there were some tickets that were not marked as complete or that were marked as v12 that I thought were no longer included. Since it's easier to delete than to go and add those tickets in later, I included everything, but please particularly look at the following tickets to make sure they should be included:

  • tickets not marked closed or merged
    • Update gliomatosis cerebri term in LGAT subtyping Ticket 358
    • Update EPN analysis to pull new gene names using GENCODE v39 symbols Ticket 485
    • Fusion summary to use new gene symbols from GENCODE v39 Ticket 486
    • HGG subtyping to include GENCODE v39 gene symbols Ticket 487
    • LGG subtyping to take in new H3 gene symbols for GENCODE v39 update Ticket 488
    • Incorrect subtypes Ticket 489
  • tickets apparently relating to PPTC PDX samples
    • Bix Dev PedcbioPortal Support: Update PPTC study reference Ticket 375
    • Create PPTC PDX study base histologies file Ticket 479

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

doc/release-notes.md

What is your summary of the results?

List of changes with tickets referenced for the v12 release

@kelseykeith
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One other note, will need to update the date of the release and the release PR before cutting the v12 release

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@jharenza jharenza left a comment

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Thanks so much for starting this- few change requests, but should be good to go soon!

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Comment on lines 8 to 17
- This release adds the following data:
- 744 methylation array data samples
- 728 PBTA samples (17 normal, 711 tumor)
- 16 TARGET samples (6 normal, 10 tumor)
- 1264 RNA-seq samples
- 1264 PBTA samples (3 normal, 1261 tumor)
- 2759 WGS/WXS samples
- 3 Kentucky samples (3 normal)
- 2441 PBTA WGS samples (1171 normal, 1270 tumor)
- 315 PBTA WXS samples (160 normal, 155 tumor)
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@zzgeng can you update this to current Ns - there is no Kentucky in this release, it is within PBTA, and we might have ~4 more PBTA in addition. thanks

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@jharenza
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merging this one without CI, documentation only!

@jharenza jharenza merged commit e8e9078 into v12-analysis-files Apr 30, 2023
@jharenza jharenza deleted the v12-release-notes branch April 30, 2023 14:56
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3 participants