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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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add missing key resources to software table S5 #1409

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Closes #1407

What was your approach?

Add 3 missing software tools, remove GISTIC from OpenPBTA-workflows repo and the workflows section of the table since it is also in the docker within the OpenPBTA repo

What GitHub issue does your pull request address?

1407

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

Which areas should receive a particularly close look?

NA

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)?

What is your summary of the results?

Reproducibility Checklist

Documentation Checklist

sjspielman commented 2 years ago

@jaclyn-taroni if you can take a peak here and see if you agree that the Table S3 diffs look ok given #1383? It looks ok to me, but more eyes is good for this.

jharenza commented 2 years ago

@sjspielman I just reran this with v22, since this PR was started with v21. I do have more updates in #1448, so I can either move the KR updates to that one, or we can merge this first, then I can rerun #1448

sjspielman commented 2 years ago

I do have more updates in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1448, so I can either move the KR updates to that one, or we can merge this first, then I can rerun https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1448

Let's focus on updating this table here, and the rest in #1448. That said, note my comment about whether this addressed #1481 too!

jharenza commented 2 years ago

closing in favor of #1448