coda4microbiome: compositional data analysis for microbiome studies

• Published in: bioRxiv
• Main Authors: Calle, Mluz, Susin, Antoni
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 11.06.2022
• Subjects: Microbiomes
• DOI: 10.1101/2022.06.09.495511

Motivation: One of the main challenges of microbiome analysis is its compositional nature that if ignored can lead to spurious results. This is especially critical when dealing with microbiome variable selection since classical differential abundance tests are known to provide large false positive rates. Results: We developed coda4microbiome, a new R package for analyzing microbiome data within the Compositional Data Analysis (CoDA) framework in both, cross-sectional and longitudinal studies. The core functions of the library are aimed at the identification of microbial signatures and involve variable selection in generalized linear models with compositional covariates. All algorithms are accompanied by meaningful graphical representations that allow a better interpretation of the results. Availability: coda4microbiome is implemented as an R package and is available at CRAN https://cran.rproject.org/web/packages/coda4microbiome/index.html. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://malucalle.github.io/coda4microbiome/