PT - JOURNAL ARTICLE AU - Bokulich, Nicholas A. AU - Zhang, Yilong AU - Dillon, Matthew AU - Rideout, Jai Ram AU - Bolyen, Evan AU - Li, Huilin AU - Albert, Paul S. AU - Caporaso, J. Gregory TI - q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data AID - 10.1101/223974 DP - 2017 Jan 01 TA - bioRxiv PG - 223974 4099 - http://biorxiv.org/content/early/2017/11/22/223974.short 4100 - http://biorxiv.org/content/early/2017/11/22/223974.full 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.