CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources

SummaryThe Biolog Phenotype Microarray (PM) and Anaerobic MicroPlates (AN) 96-well plates utilise colorimetric redox reactions to rapidly screen bacteria for the ability to utilise different carbon sources and other metabolites. Measurement of substrate utilisation as bacterial growth curves typically involves extended data normalization, outlier detection, and statistical analysis. The CarboLogR package streamlines this process with a Shiny application, guiding users from raw data generated from Biolog assays to growth profile comparison. We applied chemoinformatics approaches to define clusters of carbon sources, based on molecular similarities, increasing statistical power. Altogether, CarboLogR is a novel integrated tool providing automatic and high-level resolution for bacterial growth patterns and carbon source usage.\n\nAvailability and ImplementationCarboLogR application can be downloaded and installed from Github repository https://github.com/kevinVervier/CarboLogR. Tutorial, data, and examples can be downloaded at https://github.com/kevinVervier/CarboLogR/vignettes.\n\nContactkv4@sanger.ac.uk\n\nSupplementary InformationSupplementary data are available at Bioinformatics online.