MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

• Published in: Microbiome Vol. 6; no. 1; pp. 32 - 12
• Main Authors: Metwally, Ahmed A., Yang, Jie, Ascoli, Christian, Dai, Yang, Finn, Patricia W., Perkins, David L.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13.02.2018; BioMed Central; BMC
• Subjects: Bacteroides - classification; Bacteroides - isolation & purification; Bifidobacterium - classification; Bifidobacterium - isolation & purification; Differential abundance; Finland; Genetic aspects; Genomics; High-Throughput Nucleotide Sequencing; Humans; Infant; Longitudinal Studies; Metagenomics; Metagenomics - methods; Microbiome; Microbiota (Symbiotic organisms); Physiological aspects; RNA, Ribosomal, 16S; Russia; Smoothing splines; Software; Time series; United States; Metagenomics; Time series; Differential abundance; Smoothing splines; Longitudinal studies; Negative binomial distribution; Microbiome

Microbial longitudinal studies are powerful experimental designs utilized to classify diseases, determine prognosis, and analyze microbial systems dynamics. In longitudinal studies, only identifying differential features between two phenotypes does not provide sufficient information to determine whe...