In jasenfinch/metaboWorkflows: Workflow Project Templates for Metabolomics Analyses

knitr::opts_chunk$set(collapse = TRUE, 
                      comment = "#>",
                      fig.align = 'center',
                      fig.path = "man/figures/README-",
                      message = FALSE)
library(metaboWorkflows)

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:

availableWorkflows() %>% 
  {paste0('* ',.,collapse = '\n')} %>% 
  cat()

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.

jasenfinch/metaboWorkflows documentation built on May 24, 2023, 8:23 a.m.