This is a customised flavor of https://github.com/hexylena/docker-rstudio-notebook for Metabolomics Data Processing with R packages. Most of the code was taken from Data Integration Hackathon analyses.
Additionnal Metabolomics R packages are from RforMasspectrometry web site
- factoextra
- msdata
- mzR
- r hdf5
- lgatto/rpx
- MsCoreUtils
- QFeatures
- Spectra
- ProtGenerics
- PSMatch
- pheatmap
- limma
- MSnID
- RforMassSpectrometry/SpectraVis
##Addition of other packages
- metaMS
- msPurity
- SpectraQL
Specific Data Integration R packages are pre-installed from Data Integration Hackathon:
- MixOmics (v6.22 Bioconductor - mixOmics)
- iClusterPlus (v1.34 Bioconductor - iClusterPlus)
- MOFA2 (v1.8 Bioconductor - MOFA2)
Other pre-installed R packages:
- tidyverse (v1.3.2 CRAN - tidyverse)
- tidymodels (CRAN - tidymodels)
- targets (v0.14.1 GitHub - targets)
Other pre-installed linux system package:
- quarto (v1.2.269 Quarto - get started)
This image can be used as a Galaxy Interactive Tool.
First make sure your Galaxy instance is configured to support Interactive Tools.
Then you need to copy the ./interactivetool_rstudio_metabolomics-dataprocessing.xml file into $GALAXY_ROOT/tools/interactive/.
Add this new tool to $GALAXY_ROOT/config/tool_conf.xml:
<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
[...]
<section id="interactive_tools" name="Interactive tools">
[...]
<tool file="interactive/interactivetool_rstudio_metabolomics-dataprocessing.xml" />
</section>
</toolbox>And add this tool to $GALAXY_ROOT/config/job_conf.xml: follow the instructions in the Interactive Tools tutorial, and adapt depending on your setup.