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metaboWorkflows

Lifecycle: stable R-CMD-check Codecov test coverage license GitHub release

Workflow Project Templates for Metabolomics Analyses

Overview

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

Installation

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

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

Learn more

The package documentation can be browsed online at https://jasenfinch.github.io/metaboWorkflows/.

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 https://github.com/jasenfinch/metaboWorkflows/issues.