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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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Proposed Analysis: NBL vs GTEX batch correction and plots #40

Closed jharenza closed 1 year ago

jharenza commented 3 years ago

What are the scientific goals of the analysis?

If this PR20 is successful at batch correction (Ticket #39), re-assess NBL TARGET and GMKF vs GTEX cell surface protein TPM comparisons/plots.

What methods do you plan to use to accomplish the scientific goals?

  1. Use the RUVseq method from PR20 and the gene list here to perform batch correction. (This piece can go into the batch correction module.

  2. Add a second, staggered PR to plot TPMs of the NBL-specific immunotherapeutic targets for both NBL TARGET and NBL GMKF vs GTEX: ALK, MYCN, GPC2, CAMKV, L1CAM, NCAM1, B4GALNT1, DLL3, PHOX2B, DLK1

What input data are required for this analysis?

gtex_target_tcga-gene-counts-rsem-tpm-collapsed.rds (will come in v5) gene-counts-rsem-tpm-collapsed.rds (will have GMKF) histologies.tsv

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

1-2 days

Who will complete the analysis (please add a GitHub handle here if relevant)?

@komalsrathi

What relevant scientific literature relates to this analysis?

NA

jharenza commented 2 years ago

@komalsrathi @aadamk @sangeetashukla this is an old issue and I haven't been following https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/168 100%, but is this being investigated as a part of that PR as well?

sangeetashukla commented 2 years ago

PediatricOpenTargets/OpenPedCan-analysis#168

@jharenza I was on vacation last week, and I am back now and working on the PR you linked above, but I was not aware of this ticket. I will post an update here along with my updates on the PR#168.