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bioRxiv · 10.1101/223974

q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data

Bokulich, N.·Zhang, Y.·Dillon, M.·Rideout, J. R.·Bolyen, E.·Li, H.·Albert, P.·Caporaso, J. G.
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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 paired differences and distances, linear mixed effects models, microbial interdependence test, first differencing, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open source software released under a BSD-3-Clause license and is freely available, including for commercial use.

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Bokulich, N., Zhang, Y., Dillon, M., Rideout, J. R., Bolyen, E., Li, H., Albert, P., Caporaso, J. G.. 2017-11-22. q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data. https://doi.org/10.1101/223974

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