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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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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. |
format | Online Article Text |
id | pubmed-5859990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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