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:

LessonSlidesHands-onInput datasetWorkflowsGalaxy tour
Introduction to Metabolomics
Mass spectrometry imaging: Examining the spatial distribution of analytes
Mass spectrometry imaging: Finding differential analytes
Mass spectrometry: LC-MS analysis

Available Tools

Workflow4Metabolomics Tools

ToolDescription
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
normalizationNormalization (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.
ToolDescription
w4mclassfilterFilter W4M data by values or metadata
w4mjoinpnJoin positive- and negative-mode W4M datasets
w4mcorcovOPLS-DA Contrasts of Univariate Results

Gateways

Other metabolomics specialized Galaxy servers:

Servers
Workflow4Metabolomics
PhenoMeNal

News and Events

Galaxy 2026 update published in Nucleic Acids Research
News More news
Events More events

Contributors

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Our Data Policy

Registered UsersUnregistered UsersFTP DataGDPR 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.