Any R package to check the expression of single gene in multiple cancer types of TCGA?

Question

[Biologist]

I'm interested in one lncRNA. And would like to check its expression between tumor and normal in all cancer types of TCGA. Usually for protein coding genes I use cbioportal. But some genes and lncRNAs information is not found in that.

So, are there any R packages to check the expression of an interested gene/lncRNA in pan cancer wise?

Answer 1

[Kevin Blighe]

You can simply try the other tools, such as TCGAbiolinks, RTCGA, USCSXenaTools (each a package in R), et cetera. cBioPortal does have lncRNAs, but perhaps not the ones in which you are interested. Note that each of these tools is essentially a third-party and most or all take the TCGA data hosted on Genomic Data Commons and re-process it in their own style. If I need TCGA data, I typically take it direct from Genomic Data Commons.

Kevin

[Biologist]

But for TCGAbiolinks or RTCGA or other tools have to download all the complete data for all cancer types and then check the specific lncRNA expression. Is it possible to get only expression of that particular gene for all cancer types at a time?

[Kevin Blighe]

Why would that be a problem? You would then have the data for future use whenever you needed it.