AUTHOR=Shields-Cutler Robin R. , Al-Ghalith Gabe A. , Yassour Moran , Knights Dan TITLE=SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies JOURNAL=Frontiers in Microbiology VOLUME=9 YEAR=2018 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.00785 DOI=10.3389/fmicb.2018.00785 ISSN=1664-302X ABSTRACT=

Longitudinal, prospective studies often rely on multi-omics approaches, wherein various specimens are analyzed for genomic, metabolomic, and/or transcriptomic profiles. In practice, longitudinal studies in humans and other animals routinely suffer from subject dropout, irregular sampling, and biological variation that may not be normally distributed. As a result, testing hypotheses about observations over time can be statistically challenging without performing transformations and dramatic simplifications to the dataset, causing a loss of longitudinal power in the process. Here, we introduce splinectomeR, an R package that uses smoothing splines to summarize data for straightforward hypothesis testing in longitudinal studies. The package is open-source, and can be used interactively within R or run from the command line as a standalone tool. We present a novel in-depth analysis of a published large-scale microbiome study as an example of its utility in straightforward testing of key hypotheses. We expect that splinectomeR will be a useful tool for hypothesis testing in longitudinal microbiome studies.