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d3b-center / hope-cohort-analysis

Analysis for HOPE cohort
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GSVA analysis of proteomics data #79

Closed JosephDybas closed 4 months ago

JosephDybas commented 8 months ago

This commit includes the code to run GSVA analysis on the whole cell proteomics data for the HOPE cohort. The GSVA R library is implemented to run the GSVA enrichment analysis. The Kids First IDs are changed to sample IDs (SG IDs) in order to compare to other data and established cell lines.

jharenza commented 7 months ago

@JosephDybas I think this is ready for another look by you

jharenza commented 7 months ago

hi @JosephDybas can you merge master/main into this and rerun?

JosephDybas commented 7 months ago

hi @JosephDybas can you merge master/main into this and rerun?

I think merging is blocked until @zzgeng reviews. Thanks!

jharenza commented 7 months ago

hi @JosephDybas can you merge master/main into this and rerun?

I think merging is blocked until @zzgeng reviews. Thanks!

Sorry- I didn't mean merge the PR. I meant merge the main branch into this PR, update your code to intake the new files which aren't lifted over, and rerun so it can be re-reviewed. Last step before any merge TO main must be merging main into your branch and if any conflicts/updates required for rerun, then rerun. Let me know if we can help.

komalsrathi commented 6 months ago

@JosephDybas I forgot to add your name to the authors' list in the README. If possible, can you add your name to the README in this PR?

JosephDybas commented 5 months ago

Re-ran GSVA analysis on non-liftover proteomics data.