2018
https://cran.rstudio.com/bin/linux/ubuntu/Install latest GNU R version 3.3.2 on Linux1) Add CRAN repositorya) Ubuntu 16
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 b) Debian
https://cran.rstudio.com/bin/linux/debian/ 2) Install Rsudo apt-get update sudo apt-get install r-base
sudo apt-get install libcurl4-openssl-dev # required for DESeq2 (annotate -> RCurl) 3) Install R packages DESeq2 & CSSDESeq2 is required indifferential_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") # for CSS norm, see also: -> how to install biom > biocLite("metagenomeSeq") # required for CSS normalization> biocLite("biomformat") > biocLite("randomForest") # required for supervised_learning.py> q() # exit RSave workspace image? [y/n/c]: n
|