Install R locally with anaconda to use ballgown for RNA-Seq

Just a mail I just send to a couple of colleagues, explaining how I installed the RNA-Seq analysis package ballgown on a unxi debian "Jessie".
Should in general work for unix.



Hello,

after mapping the RNA-Seq reads with Hisat2
and calculating transcripts and readcounts with stringtie
it is time to analyse the data with 

ballgown
https://github.com/alyssafrazee/ballgown


First it needs to be installed.
This doesn't work straight-forward, because you can not install it in
the default R. At least for me it didn't work.

This is how I did it:

install anaconda (this automatically installs a local R version in
/home/ries/anaconda2/)
 
https://docs.continuum.io/anaconda/install


install very important R packages:
> I found the command to install a number of famous R packages: conda
> install -c r r-essentials

it also automatically installs the bioconductor installer,
which can then be used to install ballgown:

start your local R:
/home/ries/anaconda2/bin/R

and from within R:
source("http://bioconductor.org/biocLite.R")
biocLite("ballgown")


Good bye from
ries@home