Bubble

World Wide Web

Workflow

Statistics

Web application

R package

Operating system

The Internet

Set (abstract data type)

Computer science

Code (set theory)

Maximum bubble pressure method

Database

Mathematics

Interface (matter)

Web server

Programming language

Flexibility (engineering)

Bioinformatics

Summary The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data. Availability and implementation MetaboAnalystR is freely available from https://github.com/xia-lab/MetaboAnalystR.

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data