Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

riboviz: analysis and visualization of ribosome profiling datasets

Oana Carja, Tongji Xing, Joshua B. Plotkin, Premal Shah
doi: https://doi.org/10.1101/100032
Oana Carja
1Department of Biology, University of Pennsylvania, Philadelphia, 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: ocarja@sas.upenn.edu
Tongji Xing
2Department of Genetics, Rutgers University, Piscataway, NJ, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joshua B. Plotkin
1Department of Biology, University of Pennsylvania, Philadelphia, 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Premal Shah
2Department of Genetics, Rutgers University, Piscataway, NJ, USA
3Human Genetics Institute of New Jersey, Piscataway, NJ, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: premal.shah@rutgers.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. We developed a processing pipeline and browser-based visualization, riboviz, that allows convenient exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible backend analysis pipeline that allows the user to analyze their private unpublished dataset, along with a web application for comparison with previously published public datasets.

Availability and implementation JavaScript and R source code and extra documentation are freely available from https://github.com/shahpr/RiboViz, while the web-application is live at www.riboviz.org.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted January 12, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
riboviz: analysis and visualization of ribosome profiling datasets
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
riboviz: analysis and visualization of ribosome profiling datasets
Oana Carja, Tongji Xing, Joshua B. Plotkin, Premal Shah
bioRxiv 100032; doi: https://doi.org/10.1101/100032
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
riboviz: analysis and visualization of ribosome profiling datasets
Oana Carja, Tongji Xing, Joshua B. Plotkin, Premal Shah
bioRxiv 100032; doi: https://doi.org/10.1101/100032

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4105)
  • Biochemistry (8807)
  • Bioengineering (6509)
  • Bioinformatics (23446)
  • Biophysics (11783)
  • Cancer Biology (9198)
  • Cell Biology (13312)
  • Clinical Trials (138)
  • Developmental Biology (7429)
  • Ecology (11402)
  • Epidemiology (2066)
  • Evolutionary Biology (15141)
  • Genetics (10430)
  • Genomics (14036)
  • Immunology (9167)
  • Microbiology (22142)
  • Molecular Biology (8802)
  • Neuroscience (47533)
  • Paleontology (350)
  • Pathology (1427)
  • Pharmacology and Toxicology (2489)
  • Physiology (3729)
  • Plant Biology (8076)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2220)
  • Systems Biology (6036)
  • Zoology (1252)