\[!\[Build Status\](https://github.com/computational-metabolomics/metabolomicsWorkbenchR/workflows/metabolomicsWorkbenchR/badge.svg)\](https://github.com/computational-metabolomics/metabolomicsWorkbenchR/actions) \[!\[Codecov test coverage\](https://codecov.io/gh/computational-metabolomics/metabolomicsWorkbenchR/branch/master/graph/badge.svg)\](https://codecov.io/gh/computational-metabolomics/metabolomicsWorkbenchR?branch=master) # metabolomicsWorkbenchR A Bioconductor package for interfacing with the Metabolomics Workbench API (https://www.metabolomicsworkbench.org/). ## Installation To install this package, start R (version "4.0") and enter: \`\`\`{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("metabolomicsWorkbenchR") \`\`\` Alternatively, to install from github use the \`remotes\` package, where \`@master\` can be replaced with release tags if desired: \`\`\`{r} remotes::install\_github('computational-metabolomics/metabolomicsWorkbenchR@master') \`\`\` ## Introduction This package enables access to the Metabolomics Workbench API (MWA) using a simple query interface. For example, the 'study' context can be queried using the 'study\_title' input to search the database for all studies with the keyword 'Diabetes' in the title and return a summary: \`\`\`{r} library(metabolomicsWorkBench) df = do\_query(context = 'study', input\_item = 'study\_title', input\_value = 'Diabetes', output\_item = 'summary') \`\`\` The query interface is designed to mirror the API documentation as closely as possible (https://www.metabolomicsworkbench.org/tools/MWRestAPIv1.0.pdf). Methods have been included using multiple queries to coerce study data from the database into different data structures used within Bioconductor, namely \`SummarizedExperiment\` and \`MultiAssayExperiment\`. In addition methods have been included to coerce study data into \`DatasetExperiment\` objects for compatibility with our \`struct\` and \`structToolbox\` packages (both available on Bioconductor).