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R for QIIME

Install latest GNU R version 3.3.2 on Linux

1) Add CRAN repository

a) Ubuntu
sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
https://cran.rstudio.com/bin/linux/ubuntu/

b) Debian
sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/"
gpg --keyserver pgp.mit.edu --recv-key 381BA480
gpg -a --export 381BA480 | apt-key add -
https://cran.rstudio.com/bin/linux/debian/

2) Install R

sudo apt-get update
sudo apt-get install r-base
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev # required for DESeq2 (annotate -> RCurl)

3) Install R packages DESeq2 & CSS

DESeq2 is required in differential_abundance.py
CSS is required in normalize_table.py

Start R and install packages:
sudo R
> source("http://bioconductor.org/biocLite.R")
> biocLite("DESeq2")
Update all/some/none? [a/s/n]: a     # yes, update all old R-packages
> biocLite("optparse")
> biocLite("biom")
> biocLite("metagenomeSeq") # required for CSS normalization
> biocLite("biomformat")
> biocLite("randomForest")  # required for supervised_learning.py
> q()   # exit R
Save workspace image? [y/n/c]: n