Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification

Abstract Summary Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers—such as Kraken, Centrifuge and MethaPhlAn—using interactive data tables, heatmaps and Sankey...

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Published in	Bioinformatics Vol. 36; no. 4; pp. 1303 - 1304
Main Authors	Breitwieser, Florian P, Salzberg, Steven L
Format	Journal Article
Language	English
Published	England Oxford University Press 15.02.2020
Subjects	Applications Notes Data Interpretation, Statistical Metagenomics Microbiota Software
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Abstract	Abstract Summary Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers—such as Kraken, Centrifuge and MethaPhlAn—using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection. Availability and implementation Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.
AbstractList	Abstract Summary Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers—such as Kraken, Centrifuge and MethaPhlAn—using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection. Availability and implementation Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian. Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection.SUMMARYPavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection.Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.AVAILABILITY AND IMPLEMENTATIONPavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian. Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection. Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.
Author	Salzberg, Steven L Breitwieser, Florian P
AuthorAffiliation	1 Center for Computational Biology, Whiting School of Engineering , Johns Hopkins University, Baltimore, MD, USA 2 Departments of Biomedical Engineering, Computer Science and Biostatistics , Johns Hopkins University, Baltimore, MD, USA
AuthorAffiliation_xml	– name: 1 Center for Computational Biology, Whiting School of Engineering , Johns Hopkins University, Baltimore, MD, USA – name: 2 Departments of Biomedical Engineering, Computer Science and Biostatistics , Johns Hopkins University, Baltimore, MD, USA
Author_xml	– sequence: 1 givenname: Florian P surname: Breitwieser fullname: Breitwieser, Florian P email: pavianviz@gmail.com organization: Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA – sequence: 2 givenname: Steven L surname: Salzberg fullname: Salzberg, Steven L organization: Departments of Biomedical Engineering, Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/31553437$$D View this record in MEDLINE/PubMed
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Snippet	Abstract Summary Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze,... Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform...
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SubjectTerms	Applications Notes Data Interpretation, Statistical Metagenomics Microbiota Software
Title	Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
URI	https://www.ncbi.nlm.nih.gov/pubmed/31553437 https://www.proquest.com/docview/2297128602 https://pubmed.ncbi.nlm.nih.gov/PMC8215911
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