This analysis requires tools, parallel, data.table, devtools, phyloRNA and beter packages.
Packages tools and parallel are part of standard install of R do not need to be installed manually.
Packages data.table and devtools are available from CRAN. First, start R console by typing R into terminal:
R
and now type:
install.packages("data.table")
install.packages("devtools")
Packages might have additional system requirements that will not be automatically installed by R. You would need to find them in the error log and install them manually. On ubuntu, start terminal and run:
sudo apt install name-of-library
Alternatively, you could install these packages with the conda, start terminal and type:
conda install r-devtools r-data.table
This should automatically install all required system libraries.
These packages are not available on CRAN. You can however easily install them directly from github using the devtools package. Start the R console and type:
devtools::install_github("biods/phyloRNA")
devtools::install_github("biods/beter")
this will automatically install these packages and required dependencies.
To install the pysam package, simply type into the terminal:
pip install pysam