Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
- DESeq2
- edgeR
- fdrtool
We strongly recommend that you install Riborex via conda:
conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed. Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version "riborex-x.x.x.tar.gz" from releases at https://github.com/smithlabcode/riborex, start a terminal and CD into the directory where you downloaded Riborex, start R and enter
install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools
package and then install
riborex
to get latest changes :
install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
Please refer to vignettes/riborex.pdf for how to use riborex.
Andrew D. Smith [email protected]
Wenzheng Li [email protected]
Weili Wang [email protected]
If you found a bug or mistake in this project, we would like to know about it. Before you send us the bug report though, please check the following:
- Are you using the latest version? The bug you found may already have been fixed.
- Check that your input is in the correct format and you have selected the correct options.
- Please reduce your input to the smallest possible size that still produces the bug; we will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be.
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.