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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data.
- Source :
-
MSystems [mSystems] 2018 Nov 20; Vol. 3 (6). Date of Electronic Publication: 2018 Nov 20 (Print Publication: 2018). - Publication Year :
- 2018
-
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.
Details
- Language :
- English
- ISSN :
- 2379-5077
- Volume :
- 3
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- MSystems
- Publication Type :
- Academic Journal
- Accession number :
- 30505944
- Full Text :
- https://doi.org/10.1128/mSystems.00219-18