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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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Updated analysis: subset each-cohort independent primary tumor RNA-seq samples in `tumor-gtex-plots` module #169

Closed logstar closed 2 years ago

logstar commented 3 years ago

What analysis module should be updated and why?

The tumor-gtex-plots module should be updated to subset each-cohort independent primary tumor RNA-seq samples before generating plots/results. The motivation is to have only one primary tumor RNA-seq sample for each patient of each cohort in the plots/results.

The list of each-cohort independent primary tumor RNA-seq samples (analyses/independent-samples/results/independent-specimens.rnaseq.primary.eachcohort.tsv) is generated in the independent-samples module, essentially by selecting only one primary tumor RNA-seq sample for each patient in each cohort.

What changes need to be made? Please provide enough detail for another participant to make the update.

Subset RNA-seq samples in gene-expression-rsem-tpm-collapsed.rds before generating plots/results.

What input data should be used? Which data were used in the version being updated?

Input data for tumor-gtex-plots.

analyses/independent-samples/results/independent-specimens.rnaseq.primary.eachcohort.tsv.

When do you expect the revised analysis will be completed?

1-3 days

Who will complete the updated analysis?

@komalsrathi

cc @jharenza

logstar commented 3 years ago

Hi @komalsrathi . Same note as in #171 .

I added blocked label to this issue, because the tumor-gtex-plots module development/maintenance will temporarily be suspended. The tumor-gtex-plots module will be updated at a later point to switch from R API to javascript boxplots.

The code in tumor-gtex-plots will be used to develop an R API at https://github.com/PediatricOpenTargets/OpenPedCan-api by @taylordm and @logstar for PedOT website demo or production.

komalsrathi commented 3 years ago

@logstar will we be still doing this for the tumor-gtex-plots module?

logstar commented 3 years ago

@logstar will we be still doing this for the tumor-gtex-plots module?

I think we probably will do this when FNL is shifting from the API server to javascript plots.

cc @jharenza