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# Welcome to **UseGalaxy.EU Metabolomics**
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<strong>Metabolomics.UseGalaxy.eu</strong> is a community driven metabolomics Galaxy service. The main aim is to give people a public space to discover and run metabolomics tools. If there is something that should be added, please let us know on [Gitter](https://gitter.im/usegalaxy-eu/Lobby).

During the [2019 Galaxy Community Conference](https://galaxyproject.org/events/gcc2019/) (GCC2019) metabolomics users and developers are invited to meet during a Birds of a Feather (BoF) event to plan the aims of this service.

# Content
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1. TOC
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# Get started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface.

# Training

Want to learn more about metabolomics? Check out the following lesson tutorials from the [Galaxy Trainings Network](https://galaxyproject.github.io/training-material/topics/metabolomics/){:target="_blank"}:

Lesson | Slides | Hands-on | Input dataset | Workflows | Galaxy tour
--- | --- | --- | --- | --- | ---
Introduction to Metabolomics | [<i class="fa fa-slideshare" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/metabolomics/slides/introduction.html){:target="_blank"} | | | |
Mass spectrometry imaging: Examining the spatial distribution of analytes | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html){:target="_blank"} | [<i class="fa fa-topic" aria-hidden="true"></i>](https://zenodo.org/record/484496){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>](https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/){:target="_blank"} |
Mass spectrometry imaging: Finding differential analytes | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html){:target="_blank"} | [<i class="fa fa-topic" aria-hidden="true"></i>](https://zenodo.org/record/2628280){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>](https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/){:target="_blank"} |
Mass spectrometry: LC-MS analysis | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/tutorial.html){:target="_blank"} | [<i class="fa fa-topic" aria-hidden="true"></i>](https://zenodo.org/record/3244991){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>](https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/lcms/workflows/){:target="_blank"} |
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# Available Tools

## Workflow4Metabolomics Tools

Tool | Descirption
--- | ---
[xcms_xcmsset](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files
[xcms_group](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together
[xcms_retcor](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples
[lipidmaps_textsearch](https://github.com/workflow4metabolomics/tool-bank-lipidmaps.git) | [W4M][LC-MS] LIPID MAPS Structure Database (LMSD) - Annotation - Returns annotation results from LIPID MAPS Structure Database and its Text/Ontology-based search engine.
[probmetab](https://toolshed.g2.bx.psu.edu/view/mmonsoor/probmetab) | [W4M][LC-MS] ProbMetab - automatic probabilistic LC-MS based metabolome annotation
[profia](https://github.com/workflow4metabolomics/profia.git) | [W4M][FIA-HRMS] Preprocessing of Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) data.
[xcms_fillpeaks](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks
[camera_annotate](https://toolshed.g2.bx.psu.edu/view/lecorguille/camera_annotate) | [W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results (isotope peaks, adducts and fragments)
[xcms_merge](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - Merge individual xcmsSet outputs
[generic_filter](https://toolshed.g2.bx.psu.edu/view/melpetera/generic_filter) | [W4M][Utils] Filtering according to specific variables
[xcms_summary](https://github.com/workflow4metabolomics/xcms) | [W4M][LC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS and CAMERA analysis
[camera_combinexsannos](https://toolshed.g2.bx.psu.edu/view/mmonsoor/camera_combinexsannos) | [W4M][LC-MS] CAMERA R Package - Annotation - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
[batchcorrection](https://github.com/workflow4metabolomics/batchcorrection.git) | [W4M][LC-MS] Correction of data intensities for signal drift and batch-effects.
[qualitymetrics](https://github.com/workflow4metabolomics/qualitymetrics.git) | [W4M][LC-MS] Metrics and graphics to check the quality of the data.
[hmdb_ms_search](https://toolshed.g2.bx.psu.edu/view/fgiacomoni/hmdb_ms_search) | [W4M][LC-MS] HMDB database MS Search Package - Annotation - Returns annotation results (adducts and metabolites) from The Human Metabolome Database.
[univariate](https://github.com/workflow4metabolomics/univariate.git) | [W4M][LC-MS][GC-MS][NMR] Univariate statistics.
[lcmsmatching](https://github.com/workflow4metabolomics/lcmsmatching.git) | [W4M][LC-MS] Annotate LCMS spectrum using an in-house spectra database.
[biosigner](https://github.com/workflow4metabolomics/biosigner.git) | [W4M][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data.
[multivariate](https://github.com/workflow4metabolomics/multivariate.git) | [W4M][LC-MS][GC-MS][NMR] Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA).
[metams_rungc](https://github.com/workflow4metabolomics/metaMS) | [W4M][GC-MS] metaMS R Package - GC-MS data preprocessing using metaMS package
[withinvariation](https://github.com/workflow4metabolomics) | [W4M][Statistics] mixOmics R package withinVariation function for repeated mesurement design
[nmr_preprocessing](https://toolshed.g2.bx.psu.edu/view/marie-tremblay-metatoul/nmr_preprocessing) | [W4M][NMR] NMR Preprocessing - Preprocessing (from FID to baseline correction)
[nmr_alignment](https://github.com/workflow4metabolomics/nmr_alignment) | [W4M][NMR] NMR Alignment - Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm
[nmr_bucketing](https://github.com/workflow4metabolomics/nmr_bucketing) | [W4M][NMR] NMR Bucketing - Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data
[nmr_normalization](https://github.com/workflow4metabolomics/nmr_normalization) | [W4M][NMR] NMR Normalization - Normalization (operation applied on each individual spectrum) of bucketed and integrated NMR data
[normalization](https://toolshed.g2.bx.psu.edu/view/marie-tremblay-metatoul/normalization) | Normalization (operation applied on each individual spectrum) of preprocessed data
[transformation](https://github.com/workflow4metabolomics/transformation.git) | [W4M][LC-MS][GC-MS][NMR] Transforms the dataMatrix intensity values.
[golm_ws_lib_search](https://github.com/workflow4metabolomics/tool-bank-golm-lib_search.git) | [W4M][GC-MS] Golm Metabolome Database search spectrum
[checkformat](https://github.com/workflow4metabolomics/checkformat.git) | [W4M][LC-MS][GC-MS][NMR] Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files.
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## Workflow4Metabolomics Related Tools

Tool | Descirption
--- | ---
[w4mclassfilter](https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master) | Filter W4M data by values or metadata
[w4mjoinpn](https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master) | Join positive- and negative-mode W4M datasets
[w4mcorcov](https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master) | OPLS-DA Contrasts of Univariate Results
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# Gateways

Other metabolomics specialized Galaxy servers:

| Servers |
| --- |
| [Workflow4Metabolomics](https://workflow4metabolomics.org/) |
| [PhenoMeNal](https://portal.phenomenal-h2020.eu/home) |
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# News and Events
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# Contributors

- [Mark Esler](https://github.com/eslerm)
- [Art Eschenlauer](https://github.com/eschen42)

[<img src="/assets/media/GalaxyP_logo.png" alt="GalaxyP logo"/>](https://galaxyp.org)

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