q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
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 f...
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doaj-1458e544385f418eb732eba0f9c952092020-11-24T22:05:26ZengAmerican Society for MicrobiologymSystems2379-50772018-11-0136e00219-1810.1128/mSystems.00219-18q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome DataNicholas A. BokulichMatthew R. DillonYilong ZhangJai Ram RideoutEvan BolyenHuilin LiPaul S. AlbertJ. Gregory CaporasoLongitudinal 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.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.https://doi.org/10.1128/mSystems.00219-18bioinformaticslinear mixed effectslongitudinal analysismicrobiome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nicholas A. Bokulich Matthew R. Dillon Yilong Zhang Jai Ram Rideout Evan Bolyen Huilin Li Paul S. Albert J. Gregory Caporaso |
spellingShingle |
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 mSystems bioinformatics linear mixed effects longitudinal analysis microbiome |
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 |
series |
mSystems |
issn |
2379-5077 |
publishDate |
2018-11-01 |
description |
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.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. |
topic |
bioinformatics linear mixed effects longitudinal analysis microbiome |
url |
https://doi.org/10.1128/mSystems.00219-18 |
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