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Question: Is they any R package to download processed miRNA expression levle from TCGA?
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gravatar for jack
2.1 years ago by
jack • 760
Germany
jack • 760 wrote:

Hi all,

I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any pakage such that I can use it to download data ? I tried to dowload maually from ICGC, but miRNAs are not annotated. I was wondering whether can you help me with that ?
rna-seq next-gen tca bioinformatics • 976 views
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modified 2.1 years ago by ivivek_ngs • 4.8k • written 2.1 years ago by jack • 760
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gravatar for ivivek_ngs
2.1 years ago by
ivivek_ngs • 4.8k
Seattle,WA, USA
ivivek_ngs • 4.8k wrote:

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.

ADD COMMENT • link written 2.1 years ago by ivivek_ngs • 4.8k
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