Is they any R package to download processed miRNA expression levle from TCGA?
Entering edit mode
7.1 years ago
jack ▴ 970

Hi all,

I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any package such that I can use it to download data?

I tried to download manually from ICGC, but miRNAs are not annotated.

I was wondering whether can you help me with that?

next-gen RNA-Seq tca • 2.0k views
Entering edit mode
7.1 years ago
ivivek_ngs ★ 5.2k

Yes there is one, have you tried TCGA2STAT. This should help you to get both count data or microarray intesities or even normalized expression (RPKM/FPKM) for cancer you are looking for. Just look up to the TCGA GDC portal to understand what data is first available for your desired cancer. When you say processed, I reckon it will be count data if its RNASeq and not normalized since you want to perform the statistical tests on them. However, I fear you will find more microarray intensity values on TCGA for miRNA rather than RNASeq.


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