README.md

In smithlabcode/riborex: Identification of differential translation from Ribo-seq data

Riborex

Riborex is a R package for identification of differential translation from Ribo-seq data.

Online Paper | PDF | Supplementary File

DEPENDENCIES

• DESeq2
• edgeR
• fdrtool

INSTALLATION

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')

DOCUMENTATION

Please refer to vignettes/riborex.pdf for how to use riborex.

Contacts and bug reports

Andrew D. Smith [e-mail]

Wenzheng Li [e-mail]

Weili Wang [e-mail]

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:

1. Are you using the latest version? The bug you found may already have been fixed.
2. Check that your input is in the correct format and you have selected the correct options.
3. 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 and License Information

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/.

smithlabcode/riborex documentation built on April 12, 2021, 11:46 a.m.