timeOmics: an R package for longitudinal multi-omics data integration.

ABSTRACT

MOTIVATION Multi-omics data integration enables the global analysis of biological systems and discovery of new biological insights. Multi-omics experimental designs have been further extended with a longitudinal dimension to study dynamic relationships between molecules. However, methods that integrate longitudinal multi-omics data are still in their infancy. RESULTS: We introduce the R package timeOmics, a generic analytical framework for the integration of longitudinal multi-omics data. The framework includes pre-processing, modeling and clustering to identify molecular features strongly associated with time. We illustrate this framework in a case study to detect seasonal patterns of mRNA, metabolites, gut taxa and clinical variables in patients with diabetes mellitus from the integrative Human Microbiome Project. AVAILABILITYAND IMPLEMENTATION timeOmics is available on Bioconductor and github.com/abodein/timeOmics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.