Title |
riboviz: analysis and visualization of ribosome profiling datasets
|
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Published in |
BMC Bioinformatics, October 2017
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DOI | 10.1186/s12859-017-1873-8 |
Pubmed ID | |
Authors |
Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin, Premal Shah |
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 have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets. Source code and detailed documentation are freely available from https://github.com/shahpr/RiboViz . The web-application is live at www.riboviz.org. riboviz provides a comprehensive database and analysis and visualization tool to enable comparative analyses of ribosome-profiling datasets. This toolkit will enable both the community of systems biologists who study genome-wide ribosome profiling data and also research groups focused on individual genes to identify patterns of transcriptional and translational regulation across different organisms and conditions. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 23 | 37% |
United Kingdom | 8 | 13% |
France | 3 | 5% |
Italy | 2 | 3% |
Pakistan | 1 | 2% |
Spain | 1 | 2% |
India | 1 | 2% |
Sweden | 1 | 2% |
Latvia | 1 | 2% |
Other | 2 | 3% |
Unknown | 20 | 32% |
Demographic breakdown
Type | Count | As % |
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Scientists | 39 | 62% |
Members of the public | 23 | 37% |
Science communicators (journalists, bloggers, editors) | 1 | 2% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 61 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 17 | 28% |
Researcher | 12 | 20% |
Student > Bachelor | 8 | 13% |
Student > Master | 6 | 10% |
Professor > Associate Professor | 3 | 5% |
Other | 9 | 15% |
Unknown | 6 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 23 | 38% |
Agricultural and Biological Sciences | 20 | 33% |
Computer Science | 3 | 5% |
Pharmacology, Toxicology and Pharmaceutical Science | 2 | 3% |
Social Sciences | 2 | 3% |
Other | 4 | 7% |
Unknown | 7 | 11% |