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.