Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

Motivation: Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming,...

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Detalles Bibliográficos
Autores principales: Phanstiel, Douglas H., Boyle, Alan P., Araya, Carlos L., Snyder, Michael P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173017/
https://www.ncbi.nlm.nih.gov/pubmed/24903420
http://dx.doi.org/10.1093/bioinformatics/btu379
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author Phanstiel, Douglas H.
Boyle, Alan P.
Araya, Carlos L.
Snyder, Michael P.
author_facet Phanstiel, Douglas H.
Boyle, Alan P.
Araya, Carlos L.
Snyder, Michael P.
author_sort Phanstiel, Douglas H.
collection PubMed
description Motivation: Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming, we present Sushi.R, an R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE). Sushi.R is open source and made publicly available through GitHub (https://github.com/dphansti/Sushi) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/Sushi.html). Contact: mpsnyder@stanford.edu or dphansti@stanford.edu
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spelling pubmed-41730172014-09-25 Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures Phanstiel, Douglas H. Boyle, Alan P. Araya, Carlos L. Snyder, Michael P. Bioinformatics Applications Notes Motivation: Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming, we present Sushi.R, an R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE). Sushi.R is open source and made publicly available through GitHub (https://github.com/dphansti/Sushi) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/Sushi.html). Contact: mpsnyder@stanford.edu or dphansti@stanford.edu Oxford University Press 2014-10 2014-06-05 /pmc/articles/PMC4173017/ /pubmed/24903420 http://dx.doi.org/10.1093/bioinformatics/btu379 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Phanstiel, Douglas H.
Boyle, Alan P.
Araya, Carlos L.
Snyder, Michael P.
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title_full Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title_fullStr Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title_full_unstemmed Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title_short Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
title_sort sushi.r: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173017/
https://www.ncbi.nlm.nih.gov/pubmed/24903420
http://dx.doi.org/10.1093/bioinformatics/btu379
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