Create local R library Repo
As Python packages, we suggest that users maintain an R library repo in the home directory.
Install R libraries using 'install.packages() function
Users can simply use the following command to install an R library if it is available on CRAN, the package repository features 17000+ packages:
Install R Libraries from Github
Some R packages are maintained by the authors on GitHub
, and they are not available on CRAN. in this case, you would need the install_github() function which is available in "devtool" library. If you do not have "devtools" in your home R library repo, use the following command to install it.
And then use the following command
Install R libraries from Bioconductor
Some R libraries are only available via Bioconductor, an open-source tool for analysis and comprehension of high-throughput genomic data. The installation instruction and detailed documents can be found at https://www.bioconductor.org/
For example, to install scran, using the following commands to install "BiocManager" (if not installed yet) and the library "scran"
>if (!requireNamespace("BiocManager", quietly = TRUE))
if (requireNamespace("BiocManager", quietly = TRUE))
R environments in anaconda
First load the anaconda3 module like this:
module load anaconda3
You can create an R environment in conda via this command where 'my ve name' is the name you choose for the env:
conda create -n <my_ve_name> r-essentials r-base
After downloading all of the essential R packages you can activate the enviroment via:
conda activate <my_ve_name>
The official docs for R from anaconda: https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/
-- Zhiwei- 4/2/21