R interface for .ribo files
The paper associated with this package and its larger ecosystem can be found here.
RiboR requires R version 3.6 or higher.
Install dependencies for devtools. For Ubuntu based distributions, you can use the following command.
sudo apt-get install libxml2-dev libcurl4-openssl-dev libssl-dev build-essential m4 autoconf -y
- Install devtools
install.packages("devtools")
- Load the devtools package
library("devtools")
- Install RiboR from github
install_github("ribosomeprofiling/ribor")
As it currently stands, this package lives on the devel branch, and it is not on the current release (Bioconductor 3.10). Please use the alternative installation instructions given above.
RiboR will be available via Bioconductor on the next release cycle (Bioconductor 3.11) which is scheduled for the end of April.
Once it is available, the download instructions will be as follows.
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("ribor")
Here is a walk-through of RiboR.
@article{ozadam2020riboflow,
title={RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution},
author={Ozadam, Hakan and Geng, Michael and Cenik, Can},
journal={Bioinformatics},
volume={36},
number={9},
pages={2929--2931},
year={2020},
publisher={Oxford University Press}
}