Entering edit mode
2.1 years ago
JACKY
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140
I am trying to do an analysis over Epstein Barr Virus (EBV) in R. This infection causes malignant diseases, I'm trying to associate it to some cancer type. I seek to find a gene that is required for cancer cell proliferation and/or survival.
Depmap seemed an option, I read the guide and how to use it, but I don't think it's the suitable choice for the task.
So, any suggestions for libraries in R for the job?
You make it sound so simple... a while back I transitioned from biotechnology to cancer diagnostics and I'm still at the tip of the iceberg in terms of understanding. If there was an option to pin down a single gene, the war on cancer had been won many years ago.
I'll reference some MSKCC resources because I used and know them
Beginning to define "some cancer" for example OncoTree lets you choose "884 tumor types from 32 tissues"
With regard to genes, feel free to choose among a curated list of 1066 genes at the time of writing
You're right but I need to find some association, using R. The goal is not to find new groud breaking discoveries, it's for a project so any results would do.
I'm not sure how to use this OncoTree you mentioned.
Any analysis would help, whether it's depmap, cBioPortal, really anything.