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Workflow Project Templates for Metabolomics Analyses


This package provides reproducible workflow project templates for metabolomics analyses using the hrm R package ecosystem.

These project templates utilise a number of tools to promote efficient and reproducible analysis, agnostic of the actual analysis R code. These tools include:

  • targets - an R focused pipeline toolkit for efficiently maintaining reproducible analysis workflows.
  • renv - an R package for project-local R package dependency management for maintaining reproducible R package environments.
  • git - a widely used, open-source distributed version control system.
  • docker - enables the containerization of operating system (OS) level environments. This can be used to define reproducible OS environments in which a workflow analysis can be performed.

Project templates are available for the following metabolomic techniques:

  • FIE-HRMS fingerprinting
  • NSI-HRMS fingerprinting
  • RP-LC-HRMS profiling
  • NP-LC-HRMS profiling
  • GC-MS profiling


The metaboWorkflows package can be installed from GitHub using the following:

devtools::install_github('jasenfinch/metaboWorkflows',build_vignettes = TRUE)

Learn more

The package documentation can be browsed online at

If this is your first time using metaboWorkflows see the Introduction vignette for information on how to get started.

If you believe you’ve found a bug in metaboWorkflows, please file a bug (and, if possible, a reproducible example) at