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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
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 an...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247016/ https://www.ncbi.nlm.nih.gov/pubmed/30505944 http://dx.doi.org/10.1128/mSystems.00219-18 |
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author | Bokulich, Nicholas A. Dillon, Matthew R. Zhang, Yilong Rideout, Jai Ram Bolyen, Evan Li, Huilin Albert, Paul S. Caporaso, J. Gregory |
author_facet | Bokulich, Nicholas A. Dillon, Matthew R. Zhang, Yilong Rideout, Jai Ram Bolyen, Evan Li, Huilin Albert, Paul S. Caporaso, J. Gregory |
author_sort | Bokulich, Nicholas A. |
collection | PubMed |
description | 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 | Online Article Text |
id | pubmed-6247016 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-62470162018-11-30 q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data Bokulich, Nicholas A. Dillon, Matthew R. Zhang, Yilong Rideout, Jai Ram Bolyen, Evan Li, Huilin Albert, Paul S. Caporaso, J. Gregory mSystems Methods and Protocols 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. American Society for Microbiology 2018-11-20 /pmc/articles/PMC6247016/ /pubmed/30505944 http://dx.doi.org/10.1128/mSystems.00219-18 Text en Copyright © 2018 Bokulich et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Methods and Protocols Bokulich, Nicholas A. Dillon, Matthew R. Zhang, Yilong Rideout, Jai Ram Bolyen, Evan Li, Huilin Albert, Paul S. Caporaso, J. Gregory q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data |
title | 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_short | q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data |
title_sort | q2-longitudinal: longitudinal and paired-sample analyses of microbiome data |
topic | Methods and Protocols |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247016/ https://www.ncbi.nlm.nih.gov/pubmed/30505944 http://dx.doi.org/10.1128/mSystems.00219-18 |
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