People usually go to https://omictools.com/ in order to get an idea. My advice to you, however, would be to read published manuscripts and see what the top groups in cancer have been using. There are many -really, many- bioinformatics tools out there that allow us to do just about everything. It's a skill in its own right to read published work and copy the methods, and then develop them further to suit your own needs/requirements.

Also, experience of trying out different programs is invaluable but is the best way to figure out which is best. Each program will invariably deal with a particular part of a problem better than the other programs, and I would say that it's up to us to figure out which is best.

TCGA: https://cancergenome.nih.gov/abouttcga/aboutdata/analyticaltools