RMWF

Reproducible Metabolomics Workflow (RMWF) is an R package for xcmsrocker. It provides workflow templates and demo data for different R-based metabolomics software. Users can use this package for meta-analysis across different workflows.

If you directly use the docker image, the rmwf package is already installed.

However, if you wanted to install locally on your own computer, you could install it from GitHub:

In RStudio console, input this command to install it:

# You need remotes package and you could install it by this command
install.packages('remotes')
remotes::install_github("yufree/rmwf")

Then you could find the workflow template from RStudio:

File-New file-R Markdown-from template

Then select ‘PMDDA metabolomics workflow’ to use template for PMDDA analysis.

Other template could be used to check data analysis script.

• peakpicking: from raw data to peak list

• normalization: batch correction method

• annotation: annotation from peak to peaks type or compounds

• omics: metabolomics coupled with other omics method

• statistical: statistical analysis methods

• reproducible: get data from online database

• reactomics: reactomics network analysis

• MSI: mass spectrometry imaging data analysis

Citation

• Yu, M., Dolios, G. & Petrick, L. Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features. J Cheminform 14, 6 (2022). https://doi.org/10.1186/s13321-022-00586-8