Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification-Reference-Cited by-同舟云学术

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

Published:2019-09-25 Issue:4 Volume:36 Page:1303-1304
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Breitwieser Florian P¹,Salzberg Steven L²

Affiliation:

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

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.

Funder

National Institutes of Health

U. S. Army Research Office

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz715/30138752/btz715.pdf

Reference9 articles.

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2. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts;Breitwieser;Genome Biol,2018

3. A review of methods and databases for metagenomic classification and assembly;Breitwieser;Brief. Bioinform,2017

4. Centrifuge: rapid and sensitive classification of metagenomic sequences;Kim;Genome Res.,2016

5. Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking;McMurdie;Bioinformatics,2015

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