q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

ABSTRACT Studies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sec...

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Autores principales:	Nicholas A. Bokulich, Matthew R. Dillon, Yilong Zhang, Jai Ram Rideout, Evan Bolyen, Huilin Li, Paul S. Albert, J. Gregory Caporaso
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	bioinformatics linear mixed effects longitudinal analysis microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ee7d3799c398446a9fb2f04d6677ff32
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spelling	oai:doaj.org-article:ee7d3799c398446a9fb2f04d6677ff322021-12-02T19:46:18Zq2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data10.1128/mSystems.00219-182379-5077https://doaj.org/article/ee7d3799c398446a9fb2f04d6677ff322018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00219-18https://doaj.org/toc/2379-5077ABSTRACT Studies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre-post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including interactive plotting, linear mixed-effects models, paired differences and distances, microbial interdependence testing, first differencing, longitudinal feature selection, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open-source software released under a 3-clause Berkeley Software Distribution (BSD) license and is freely available, including for commercial use. IMPORTANCE Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.Nicholas A. BokulichMatthew R. DillonYilong ZhangJai Ram RideoutEvan BolyenHuilin LiPaul S. AlbertJ. Gregory CaporasoAmerican Society for Microbiologyarticlebioinformaticslinear mixed effectslongitudinal analysismicrobiomeMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics linear mixed effects longitudinal analysis microbiome Microbiology QR1-502
spellingShingle	bioinformatics linear mixed effects longitudinal analysis microbiome Microbiology QR1-502 Nicholas A. Bokulich Matthew R. Dillon Yilong Zhang Jai Ram Rideout Evan Bolyen Huilin Li Paul S. Albert J. Gregory Caporaso q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
description	ABSTRACT Studies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre-post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including interactive plotting, linear mixed-effects models, paired differences and distances, microbial interdependence testing, first differencing, longitudinal feature selection, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open-source software released under a 3-clause Berkeley Software Distribution (BSD) license and is freely available, including for commercial use. IMPORTANCE Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.
format	article
author	Nicholas A. Bokulich Matthew R. Dillon Yilong Zhang Jai Ram Rideout Evan Bolyen Huilin Li Paul S. Albert J. Gregory Caporaso
author_facet	Nicholas A. Bokulich Matthew R. Dillon Yilong Zhang Jai Ram Rideout Evan Bolyen Huilin Li Paul S. Albert J. Gregory Caporaso
author_sort	Nicholas A. Bokulich
title	q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
title_short	q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
title_full	q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
title_fullStr	q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
title_full_unstemmed	q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
title_sort	q2-longitudinal: longitudinal and paired-sample analyses of microbiome data
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/ee7d3799c398446a9fb2f04d6677ff32
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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

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