Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The softw...

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Autores principales: Zakrzewski, Martha, Proietti, Carla, Ellis, Jonathan J, Hasan, Shihab, Brion, Marie-Jo, Berger, Bernard, Krause, Lutz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408814/
https://www.ncbi.nlm.nih.gov/pubmed/28025202
http://dx.doi.org/10.1093/bioinformatics/btw725
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author Zakrzewski, Martha
Proietti, Carla
Ellis, Jonathan J
Hasan, Shihab
Brion, Marie-Jo
Berger, Bernard
Krause, Lutz
author_facet Zakrzewski, Martha
Proietti, Carla
Ellis, Jonathan J
Hasan, Shihab
Brion, Marie-Jo
Berger, Bernard
Krause, Lutz
author_sort Zakrzewski, Martha
collection PubMed
description Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. AVAILABILITY AND IMPLEMENTATION: The web-interface is accessible via http://cgenome.net/calypso/. The software is programmed in Java, PERL and R and the source code is available from Zenodo (https://zenodo.org/record/50931). The software is freely available for non-commercial users. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-54088142017-05-03 Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions Zakrzewski, Martha Proietti, Carla Ellis, Jonathan J Hasan, Shihab Brion, Marie-Jo Berger, Bernard Krause, Lutz Bioinformatics Applications Notes Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. AVAILABILITY AND IMPLEMENTATION: The web-interface is accessible via http://cgenome.net/calypso/. The software is programmed in Java, PERL and R and the source code is available from Zenodo (https://zenodo.org/record/50931). The software is freely available for non-commercial users. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-03-01 2016-12-13 /pmc/articles/PMC5408814/ /pubmed/28025202 http://dx.doi.org/10.1093/bioinformatics/btw725 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Zakrzewski, Martha
Proietti, Carla
Ellis, Jonathan J
Hasan, Shihab
Brion, Marie-Jo
Berger, Bernard
Krause, Lutz
Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title_full Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title_fullStr Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title_full_unstemmed Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title_short Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
title_sort calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408814/
https://www.ncbi.nlm.nih.gov/pubmed/28025202
http://dx.doi.org/10.1093/bioinformatics/btw725
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