Q: How do I use a graphic from FireBrowse in my paper?
A: The FireBrowse visualization widgets (viewGene, iCoMut) do not explicitly provide a screen-capture feature; but if you use your browser's Print feature and then save the result to a PDF, you'll have a vector-graphics image than can be scaled without loss of fidelity.
Q: There area lot of
many acronyms used inFirehose and
TCGA, for example to identify disease cohorts. Where can I find what these acronyms mean?
A: Consult the TCGA Encyclopedia for general questions. There are several ways one can map cohort abbreviations to full disease names, including:
Note that our portals list 38 cohorts and the TCGA page shows 34 cohorts, with the difference being aggregate cohorts the Firehose GDAC constructed for convenience of TCGA and the research community. As of December 2016 these aggregate cohorts are:
COADREAD: colorectal, combines COAD + READ