Welcome to UseGalaxy.EU Metabolomics
Metabolomics.UseGalaxy.eu 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 Matrix.
During the 2019 Galaxy Community Conference (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
Get started
Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour through Galaxy’s user interface.
Training
Want to learn more about metabolomics? Check out the following lesson tutorials from the Galaxy Trainings Network:
Available Tools
Workflow4Metabolomics Tools
| Tool | Description |
|---|---|
| xcms_xcmsset | [W4M][LC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files |
| xcms_group | [W4M][LC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together |
| xcms_retcor | [W4M][LC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples |
| lipidmaps_textsearch | [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 | [W4M][LC-MS] ProbMetab - automatic probabilistic LC-MS based metabolome annotation |
| profia | [W4M][FIA-HRMS] Preprocessing of Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) data. |
| xcms_fillpeaks | [W4M][LC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks |
| camera_annotate | [W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results (isotope peaks, adducts and fragments) |
| xcms_merge | [W4M][LC-MS] XCMS R Package - Preprocessing - Merge individual xcmsSet outputs |
| generic_filter | [W4M][Utils] Filtering according to specific variables |
| xcms_summary | [W4M][LC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS and CAMERA analysis |
| camera_combinexsannos | [W4M][LC-MS] CAMERA R Package - Annotation - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode |
| batchcorrection | [W4M][LC-MS] Correction of data intensities for signal drift and batch-effects. |
| qualitymetrics | [W4M][LC-MS] Metrics and graphics to check the quality of the data. |
| hmdb_ms_search | [W4M][LC-MS] HMDB database MS Search Package - Annotation - Returns annotation results (adducts and metabolites) from The Human Metabolome Database. |
| univariate | [W4M][LC-MS][GC-MS][NMR] Univariate statistics. |
| lcmsmatching | [W4M][LC-MS] Annotate LCMS spectrum using an in-house spectra database. |
| biosigner | [W4M][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data. |
| multivariate | [W4M][LC-MS][GC-MS][NMR] Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA). |
| metams_rungc | [W4M][GC-MS] metaMS R Package - GC-MS data preprocessing using metaMS package |
| withinvariation | [W4M][Statistics] mixOmics R package withinVariation function for repeated mesurement design |
| nmr_preprocessing | [W4M][NMR] NMR Preprocessing - Preprocessing (from FID to baseline correction) |
| nmr_alignment | [W4M][NMR] NMR Alignment - Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm |
| 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 | [W4M][NMR] NMR Normalization - Normalization (operation applied on each individual spectrum) of bucketed and integrated NMR data |
| normalization | Normalization (operation applied on each individual spectrum) of preprocessed data |
| transformation | [W4M][LC-MS][GC-MS][NMR] Transforms the dataMatrix intensity values. |
| golm_ws_lib_search | [W4M][GC-MS] Golm Metabolome Database search spectrum |
| checkformat | [W4M][LC-MS][GC-MS][NMR] Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files. |
Workflow4Metabolomics Related Tools
| Tool | Description |
|---|---|
| w4mclassfilter | Filter W4M data by values or metadata |
| w4mjoinpn | Join positive- and negative-mode W4M datasets |
| w4mcorcov | OPLS-DA Contrasts of Univariate Results |
Gateways
Other metabolomics specialized Galaxy servers:
News and Events
- ELIXIR highlights the impact of long-term funding on Galaxy ELIXIR highlights how sustained investments in research infrastructure have supported the development and impact of Galaxy.
- In memoriam: Ross Lazarus Sorry to have drifted off but I seem to be moving out of that Galaxy and into another...
- IBSB 2026 – Bringing Galaxy Bioimage Analysis to Jena Galaxy bioimage analysis at IBSB 2026 in Jena: a symposium talk, a hands-on workshop and new tool collaborations.
- miaDash: explore microbiome data interactively in Galaxy The miaDash Shiny app from the Bioconductor microbiome team is now an interactive tool on usegalaxy.eu: import, analyse and visualise microbiome data without writing a line of code.
- Cross-disciplinary reuse of BioImage.IO AI models in Galaxy selected for the RAISE Registry of Good Practices in AI-enabled Science Galaxy's integration of BioImage.IO AI models, an example of good practice in AI-enabled science
- Workshop: Sustainable research computing with Galaxy: Workflows, infrastructure and practice - 2 daysTwo-day workshop in Madrid exploring how research workflows can be made more sustainable (19-20 November). Registration open now
- Galaxy and AI in small subjects - 2 days Mainz
- Small Scale Galaxy Admins Meeting Online, Global
- Digital Humanities Day at the University of Freiburg Freiburg
- Introduction to the Data Analysis Platform Galaxy (in German) Freiburg, Germany
Contributors
Our Data Policy
| Registered Users | Unregistered Users | FTP Data | GDPR Compliance |
|---|---|---|---|
| For all different storage options, for detailed explanations of data retention policies, and ways how to increase your quota please refer to our dedicated storage site. | Processed data will only be accessible during one browser session, using a cookie to identify your data. This cookie is not used for any other purposes (e.g. tracking or analytics). If UseGalaxy.eu service is not accessed for 90 days, those datasets will be permanently deleted. | Any user data uploaded to our FTP server should be imported into Galaxy as soon as possible. Data left in FTP folders for more than 3 months, will be deleted. | The Galaxy service complies with the EU General Data Protection Regulation (GDPR). You can read more about this on our Terms and Conditions. |