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PanViz: interactive visualization of the structure of functionally annotated pangenomes

SUMMARY: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes...

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Detalles Bibliográficos
Autores principales: Pedersen, Thomas Lin, Nookaew, Intawat, Wayne Ussery, David, Månsson, Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859990/
https://www.ncbi.nlm.nih.gov/pubmed/28057677
http://dx.doi.org/10.1093/bioinformatics/btw761
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author Pedersen, Thomas Lin
Nookaew, Intawat
Wayne Ussery, David
Månsson, Maria
author_facet Pedersen, Thomas Lin
Nookaew, Intawat
Wayne Ussery, David
Månsson, Maria
author_sort Pedersen, Thomas Lin
collection PubMed
description SUMMARY: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses. AVAILABILITY AND IMPLEMENTATION: PanViz is written entirely in JavaScript and is available on https://github.com/thomasp85/PanViz. A companion R package that facilitates the creation of PanViz visualizations from a range of data formats is released through Bioconductor and is available at https://bioconductor.org/packages/PanVizGenerator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-58599902018-03-23 PanViz: interactive visualization of the structure of functionally annotated pangenomes Pedersen, Thomas Lin Nookaew, Intawat Wayne Ussery, David Månsson, Maria Bioinformatics Applications Notes SUMMARY: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses. AVAILABILITY AND IMPLEMENTATION: PanViz is written entirely in JavaScript and is available on https://github.com/thomasp85/PanViz. A companion R package that facilitates the creation of PanViz visualizations from a range of data formats is released through Bioconductor and is available at https://bioconductor.org/packages/PanVizGenerator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-04-01 2016-12-31 /pmc/articles/PMC5859990/ /pubmed/28057677 http://dx.doi.org/10.1093/bioinformatics/btw761 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Pedersen, Thomas Lin
Nookaew, Intawat
Wayne Ussery, David
Månsson, Maria
PanViz: interactive visualization of the structure of functionally annotated pangenomes
title PanViz: interactive visualization of the structure of functionally annotated pangenomes
title_full PanViz: interactive visualization of the structure of functionally annotated pangenomes
title_fullStr PanViz: interactive visualization of the structure of functionally annotated pangenomes
title_full_unstemmed PanViz: interactive visualization of the structure of functionally annotated pangenomes
title_short PanViz: interactive visualization of the structure of functionally annotated pangenomes
title_sort panviz: interactive visualization of the structure of functionally annotated pangenomes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859990/
https://www.ncbi.nlm.nih.gov/pubmed/28057677
http://dx.doi.org/10.1093/bioinformatics/btw761
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