Question: How to get TCGA microbiota data from TCGAbiolinks (R package)
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gravatar for u107311201
7 months ago by
u1073112010
u1073112010 wrote:

As the title, I want to explore the relationship between microbiota and drug resistance events, however; I did not see any clear answer in the website. I am not familiar with the TCGAbiolinks package, I want to know if I can use it to download the 16S RNA, or any recommend package to get the microbiota data. Any one can take any example below? Thanks you!

R • 207 views
ADD COMMENTlink modified 4 weeks ago by Nitin0 • written 7 months ago by u1073112010

Try human microbiome project for raw data and for transformed data (OTU), use HMP16sData package from bioconductor.

ADD REPLYlink written 7 months ago by cpad011215k

Thank for your comment! I want to explore my project based on the TCGA. If I try the HMP16sData package from bioconductor, there have any opportunity to connect the TCGA data with the HMP16sData? And how?

ADD REPLYlink written 7 months ago by u1073112010
0
gravatar for Nitin
4 weeks ago by
Nitin0
New Delhi
Nitin0 wrote:

ftp://ftp.microbio.me/pub/cancer_microbiome_analysis/

ADD COMMENTlink written 4 weeks ago by Nitin0
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