RT Journal Article SR Electronic T1 q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data JF bioRxiv FD Cold Spring Harbor Laboratory SP 223974 DO 10.1101/223974 A1 Bokulich, Nicholas A. A1 Zhang, Yilong A1 Dillon, Matthew A1 Rideout, Jai Ram A1 Bolyen, Evan A1 Li, Huilin A1 Albert, Paul S. A1 Caporaso, J. Gregory YR 2017 UL http://biorxiv.org/content/early/2017/11/22/223974.abstract AB 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.