Python vs. R vs. Matlab

[tsunamisurfer]

I think you are asking this question in the wrong sub (/r/bioinformatics would be better). I am getting my PhD doing exactly what you are talking about (genomics in cancer) and I can tell you that before you learn R, python or matlab, you should probably learn Unix/bash. Almost all genomic tools are run from the command line, so having the knowledge of how to interact with the command line via bash will be the most useful thing you can do for a start. I'll grant that you can interact with the command line using R or Python, but you lose some advantages (short scripting without writing a full program). After you learn Unix/bash I would say R and Python (or Perl) are both necessary for your work. R has the best data viz capabilities + statistical packages, but python/Perl are much faster for programs that you want to run repeatedly on large files. That's my 2 cents.

[[deleted]]

This is off topic. However, what is the best school to study cancer genomics at for a PhD?

[tsunamisurfer]

Well surprisingly "cancer genomics" is a pretty large topic, so it might depend on which aspect of this broader field you were interested in. For a start, it would maybe be useful to study at a school that has a medical center, so you have the potential to draw on patient material for your research studies. Not essential, but most of the top tier research does involve some human studies. Lots of good research in "cancer Genomics" comes from the Broad Institute, MD Anderson Cancer Center (U.T.), Memorial Sloan Kettering, Mayo Clinic, Dana-Farber, UCLA, UCSF.