306 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
AdditiveSeries Computes an additive series to quantify a peptide in a set of samples. 4
Align Samples - Align peaks across Peaklists 1
BaselineFilter Removes the baseline from profile spectra using a top-hat filter. 3
Batch_correction Corrects intensities for signal drift and batch-effects 8
BATMAN Deconvolves resonance peaks from NMR spectra of complex mixtures and obtains concentration estimates for the corresponding metabolites automatically. 1
Biosigner Molecular signature discovery from omics data 3
Blank Filter - Remove 'blank' peaks from the biological mass spectra 1
blank-effect determines the blank effect (percentage) of each compound. 1
Boxplot of quality statistics 1
bruker2batman Converter Bruker NMR files to BATMAN converter 1
camera-annotate-peaks Generate xsAnnotate object used for further CAMERA processing. 1
camera-find-adducts Perform precursor adduct annotation using CAMERA. 1
camera-find-isotopes Perform isotope annotation using CAMERA. 1
camera-group-corr Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object. 1
camera-group-fwhm Group peaks of a xsAnnotate object according to there retention time into pseudospectra-groups. Uses the peak FWHMs as grouping borders. 1
camera-prepareoutput Prepare output for doing multi/uni variate 1
cameraToFeatureXML Converts CAMERA object to featureXML file 1
cast expand combinations of variables:values to columnar format 2
cdf2mid Starting from a set of netCDF files, it evaluates the peaks of mass isotopomer distribution (MID) for metabolites of interest, making them ready for the next step of the workflow: correction for natural isotope occurrence. 1
Change Case of selected columns 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Compare Bruker NMR/metabolites Compare specific metabolite levels in two NMR spectra 1
Compare two Datasets to find common or distinct rows 1
CompNovo Performs a de novo peptide identification using the CompNovo engine. 3
CompNovoCID Performs a de novo peptide identification using the CompNovo engine. 3
Condense consecutive characters 2
ConsensusID Computes a consensus of peptide identifications of several identification engines. 4
ConsensusMapNormalizer Normalizes maps of one consensusXML file 3
consensusXMLToXcms Converts consensusXML file to xcmsSet 1
Convert delimiters to TAB 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert DIMSpy-based HDF5 to tsv 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
Count occurrences of each record 1
Create single interval as a new dataset 1
Decharger Decharges and merges different feature charge variants of the same peptide. 3
DTAExtractor Extracts spectra of an MS run file to several files in DTA format. 4
ecomet_concentration Show concentration of species profiles 1
ecomet_download Download MTBLS study via https 1
ecomet_ecology_varpart Perform variation partitioning on study factors 1
ecomet_import_maf Import MAF file from the MTBLS study 1
ecomet_import_traits Import and process ecological characteristics file of the MTBLS study 1
ecomet_peak_picking Peak picking of the profiles in the MTBLS study 1
ecomet_phylogeny Perform phylogeny comparison analysis 1
ecomet_preparations Preparations for MTBLS study 1
ecomet_qc_extract Extract QC files from MTBLS study 1
ecomet_quality_control Quality Control of the MTBLS study 1
ecomet_raw_extract Extract RAW files from MTBLS study 1
ecomet_seasons_concentration Calculate seasons concentrations 1
ecomet_seasons_features Calculate seasons total features 1
ecomet_seasons_nmds Perform Nonmetric Multidimensional Scaling (NMDS) for the seasons 1
ecomet_seasons_rda Perform constrained distance-based redundancy analysis (dbRDA) for the factor seasons 1
ecomet_seasons_shannon Calculate Shannon diversity index for the seasons 1
ecomet_seasons_unique Calculate seasons unique features 1
ecomet_seasons_variability Show seasons variability 1
ecomet_species_diversity Generate matrix of various species diversity indices 1
ecomet_species_features Calculate species total features 1
ecomet_species_marchantia Exemplary annotation of MS1 features in the profile of Marchantia polymorpha 1
ecomet_species_rda Perform distance-based redundancy analysis (dbRDA) on the species with ecological characteristics 1
ecomet_species_shannon Calculate Shannon diversity index for the species 1
ecomet_species_unique Calculate species unique features 1
ecomet_species_variability Claculate species variability 1
ecomet_species_varpart Perform variation partitioning on the species 1
ecomet_species_venn Create Venn diagrams for seasonal variability of species features 1
EICExtractor Extracts intensities from dedicates positions in a LC/MS map 3
escher-fluxomics Visualize fluxomics data on pre-layouted metabolic maps with Escher. 1
export-measurements as sample/compound matrix. 1
ExternalCalibration Applies an external mass recalibration. 4
FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. 3
FeatureFinderCentroided Detects two-dimensional features in LC-MS data. 3
FeatureFinderIdentification Detects features in MS1 data based on peptide identifications. 3
FeatureFinderIsotopeWavelet Detects two-dimensional features in LC-MS data. 3
FeatureFinderMetabo Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 3
FeatureFinderMRM Detects two-dimensional features in LC-MS data. 3
FeatureFinderMultiplex Determination of peak ratios in LC-MS data 4
FeatureLinkerLabeled Groups corresponding isotope-labeled features in a feature map. 3
FeatureLinkerUnlabeled Groups corresponding features from multiple maps. 3
FeatureLinkerUnlabeledQT Groups corresponding features from multiple maps. 3
featureXMLToCAMERA Converts featureXML file to CAMERA 1
featureXMLToXcms Converts featureXML file to xcmsSet 1
FidoAdapter Runs the protein inference engine Fido. 5
FileConverter Converts between different MS file formats. 4
FileFilter Extracts or manipulates portions of data from peak, feature or consensus-feature files. 4
FileInfo Shows basic information about the file, such as data ranges and file type. 3
FileMerger Merges several MS files into one file. 3
Filter data on any column using simple expressions Formatting 1
Fingerprint_Clustering performs unsupervised clustering and automatically determine the best number of cluster 1
Fingerprint_Subnetwork calculates distance between metabolites in a network 1
Generic_Filter Removes elements according to numerical or qualitative values 4
Get peaklists or an average peaklist from a Peak Intensity Matrix 1
Group data by a column and perform aggregate operation on other columns. 2
HighResPrecursorMassCorrector Corrects the precursor mass and charge determined by the instrument software. 3
IDConflictResolver Resolves ambiguous annotations of features with peptide identifications 4
IDFileConverter Converts identification engine file formats. 4
IDFilter Filters results from protein or peptide identification engines based on different criteria. 3
IDMapper Assigns protein/peptide identifications to features or consensus features. 3
IDMerger Merges several protein/peptide identification files into one file. 3
IDPosteriorErrorProbability Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 3
IDRipper Split protein/peptide identification file into several files according to annotated file origin. 3
IDRTCalibration Can be used to calibrate RTs of peptide hits linearly to standards. 3
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
InclusionExclusionListCreator Creates inclusion and/or exclusion lists. 3
InspectAdapter Annotates MS/MS spectra using Inspect. 4
InternalCalibration Applies an internal mass recalibration. 4
is-rsd determines RSD of the internal standard(s). 1
ISA to mzData Extract mzData files from an ISA dataset and output a collection of mzData dataset. 1
ISA to mzML Extract mzML files from an ISA dataset and output a collection of mzML dataset. 1
ISA to mzXML Extract mzXML files from an ISA dataset and output a collection of mzXML dataset. 1
ISA to netCDF Extract netCDF files from an ISA dataset and output a collection of netCDF dataset. 1
ISA to nmrML Extract nmrML files from an ISA dataset and output a collection of nmrML dataset. 1
ISA to W4M Convert ISA data type into W4M format 1
isa_factors_viz Produce a visualization of study factors and groups from an ISA study. 1
isa_get_factors_summary Produce a summary table of variable factors of a ISA study 1
isacreate_metabo Create ISA templates for metabolomics based on study design information. 1
ISAslicer2 Query and get a slice of data files from an ISA study 1
ISAslicer2_data_filter Filters data files based on ISAslicer2 slices 1
isatab2json Converts an ISA-Tab to ISA-JSON 1
isatab_validator Produce a validation report on an ISA-Tab ZIP archive 1
iso2flux 13C Metabolic Flux Analysis on a sub-network of a large scale model. 1
IsobaricAnalyzer Calculates isobaric quantitative values for peptides 3
isodyn C++ program simulating the dynamics of metabolites and their isotopic isomers in central metabolic network using kinetic model 1
iterative-signature-algorithm Iterative Signature Algorithm [ISA] 1
ITRAQAnalyzer Calculates iTRAQ quantitative values for peptides 1
Join two Datasets side by side on a specified field 2
LC/MS matching Annotation of MS peaks using matching on a spectra database. 7
Line/Word/Character count of a dataset 1
LuciphorAdapter Modification site localisation using LuciPHOr2. 3
map-msms2camera Map MS/MS spectra to CAMERA annotations by retention time and m/z information. 1
MapAlignerIdentification Corrects retention time distortions between maps based on common peptide identifications. 2
MapAlignerPoseClustering Corrects retention time distortions between maps using a pose clustering approach. 3
MapAlignerSpectrum Corrects retention time distortions between maps by spectrum alignment. 2
MapNormalizer Normalizes peak intensities in an MS run. 3
MapRTTransformer Applies retention time transformations to maps. 4
MapStatistics Extract extended statistics on the features of a map for quality control. 3
MascotAdapter Annotates MS/MS spectra using Mascot. 3
MascotAdapterOnline Annotates MS/MS spectra using Mascot. 3
MassTraceExtractor Detects mass traces in centroided LC-MS data. 2
melt collapse combinations of variables:values to single lines 2
Merge Columns together 2
Merge peaklists produced by the tools 'Process scans (and SIM-Stitch)' or 'Replicate filter' 1
Metabolab Processing vendor raw data for Multivariate analysis 1
Metabolights downloader Import public and private MetaboLights studies 1
MetaboLights Labs Uploader Uploads data to a user workspace's within the MetaboLights Labs staging area at the European Bioinformatics Institute (EBI). 1
Metabolite_ID_Converter Enrich Metabolomic output datasets 1
metabomatching metabomatching 1
metfrag-aggregatemetfrag Aggregate results from MetFrag 1
metfrag-cli-batch Run MetFrag with a given parameter set. 1
metfrag-cli-batch-multiple Run MetFrag with a multiple parameter set on one node. 1
metfrag-passatuttoPEP Convert Metfrag scores to PEP 1
metfrag-vis Generate a PDF summary for MetFrag result files 1
metfrag-vis-multiple Generate a PDF summary for MetFrag result files. 1
metfragcli Run a single MetFrag query given a MS/MS peak list and the precursor m/z or molecular formula. 1
midcor corrects 13C mass isotopomers spectra of metabolites for natural occurring isotopes and peaks overlapping. 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MRMMapper MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 3
ms-vfetc is able to convert MS vendor exports to a generic tabular file. 1
msconvert2 Converts vendor RAW MS to mzML. 1
MSGFPlusAdapter MS/MS database search using MS-GF+. 4
msms2metfrag Generate MetFrag parameters given MS/MS spectral information and CAMERA adduct annotation. 1
msms2metfrag-multiple Generate MetFrag parameters (merged in one file) given MS/MS spectral information and CAMERA adduct annotation. 1
msnbase-filter-merge-msms Filter and merge MS/MS spectra using retention time and m/z information. 1
msnbase-read-msms Read MS/MS spectra from mzML file(s). 1
mtbls_nmr_raw_importer Import NMR data from MetaboLights 1
Multivariate PCA, PLS and OPLS 7
mw2isatab A tool to obtain an ISA document from NIH Metabolomics Workbench 1
MyriMatchAdapter Annotates MS/MS spectra using MyriMatch. 1
mzml2isa Parser to get meta information from mzML files and create an ISA-Tab structure 1
MzTabExporter Exports various XML formats to an mzTab file. 3
nmrML2BATMAN Converter nmrML files to BATMAN converter 1
nmrml2isa Parser to get meta information from nmrML files and create an ISA-Tab structure 1
nmrmlconv Converts vendor NMR RAW data to nmrML format. 1
NoiseFilterGaussian Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 3
NoiseFilterSGolay Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. 4
Normalization Normalization of (preprocessed) spectra 3
OMSSAAdapter Annotates MS/MS spectra using OMSSA. 1
OpenSwathAnalyzer Picks peaks and finds features in an SRM experiment. 3
OpenSwathAssayGenerator Generates assays according to different models for a specific TraML 3
OpenSwathChromatogramExtractor Extract chromatograms (XIC) from a MS2 map file. 2
OpenSwathConfidenceScoring Compute confidence scores for OpenSwath results 4
OpenSwathDecoyGenerator Generates decoys according to different models for a specific TraML 4
OpenSwathFeatureXMLToTSV Converts a featureXML to a mProphet tsv. 3
OpenSwathRTNormalizer This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 4
PAPY Power Analysis Tool 1
Paste two files side by side 1
Pathway_Enrichment predicts differences in metabolomic pathway expression among a (human) network (Recon v2.03) Database comparison Enrichment analysis 1
PeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
PeakPickerWavelet Finds mass spectrometric peaks in profile mass spectra. 4
PepNovoAdapter Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. 1
PeptideIndexer Refreshes the protein references for all peptide hits. 3
PhosphoScoring Scores potential phosphorylation sites in order to localize the most probable sites. 3
plot-compounds plots the retention time shifts, area, internal standard, and qc-corrected information of all compounds. 1
PrecursorIonSelector PrecursorIonSelector 3
PrecursorMassCorrector Corrects the precursor entries of MS/MS spectra, by using MS1 information. 4
Process Scans (and SIM-Stitch) - Read, filter and average MS scans 1
ProteinInference Protein inference based on the number of identified peptides. 3
ProteinQuantifier Compute peptide and protein abundances 3
ProteinResolver protein inference 3
PTModel Trains a model for the prediction of proteotypic peptides from a training set. 3
PTPredict predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel 3
qc-correction applies qc-correction to the data. 1
qc-rsd determines RSD QC. 1
Quality Metrics Metrics and graphics to check the quality of the data 4
ramid Evaluates the peaks of mass isotopomer distribution (MID), making them ready for correction for natural isotope occurrence. 1
Remove beginning of a file 1
rep-rsd determines RSD replicates. 1
Replicate Filter - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates 1
rnmr1d Preprocessing RAW NMR data with macro-commands. 1
rnmr1d-prepare-output Prepare output to be used for statistics 1
rnmr1d-stacked-plot Draw stacked plot of NMR FID. 1
rt-shifts calculates retention time shifts. 1
RTModel Trains a model for the retention time prediction of peptides from a training set. 3
RTPredict Predicts retention times for peptides using a model trained by RTModel. 3
Sample Filter - Remove peaks that fail to appear in x-out-of-n (biological) samples 1
save_chromatogram Saves the chromatogram in CSV format of an mzML, mzXML, mzData or netCDF file. 1
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
SeedListGenerator Generates seed lists for feature detection. 2
Select lines that match an expression 1
Select random lines from a file 2
show_chromatogram Show the base peak chromatogram of a raw mzML, mzXML, mzData or netCDF file. 1
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Sort data in ascending or descending order 2
Species NMDS Perform NMDS on species 1
SpecLibSearcher Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. 2
SpectraFilterBernNorm Applies thresholdfilter to peak spectra. 3
SpectraFilterMarkerMower Applies thresholdfilter to peak spectra. 3
SpectraFilterNLargest Applies thresholdfilter to peak spectra. 4
SpectraFilterNormalizer Normalizes intensity of peak spectra. 4
SpectraFilterParentPeakMower Applies thresholdfilter to peak spectra. 3
SpectraFilterScaler Applies thresholdfilter to peak spectra. 3
SpectraFilterSqrtMower Applies thresholdfilter to peak spectra. 3
SpectraFilterThresholdMower Applies thresholdfilter to peak spectra. 4
SpectraFilterWindowMower Applies thresholdfilter to peak spectra. 3
SpectraMerger Merges spectra (each MS level separately), increasing S/N ratios. 4
Summary Statistics for any numerical column 3
TextExporter Exports various XML formats to a text file. 3
TMTAnalyzer Calculates TMT quantitative values for peptides 1
TOFCalibration Applies time of flight calibration. 3
Transformation Transforms the dataMatrix intensity values 4
Trim leading or trailing characters 1
Univariate Univariate statistics 6
Unzip Data Collection Create a collection by unzipping a zip archive. 1
Upload File from your computer 2
Wiggle to Interval 1
xcms-blankfilter Filters out the peaks that have higher intensities in blank samples compare to selected samples. 1
xcms-collect-peaks Combine XCMS-Set objects into one collection used for further processing. 1
xcms-correct-rt Correct differences between retention times between different samples using the `retcor` generic method. 1
xcms-dilutionfilter Filters out the peaks that do not correlate with a dilution trend. 1
xcms-fill-peaks For each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak. 1
xcms-find-peaks Find peaks in mzML file and generate a xcmsSet using XCMS centWave algorithm. 1
xcms-group-peaks Group (or align) peaks using the XCMS `group` generic method. 1
xcmssplit Split xcmsSet collection into several objects used for further processing. 1
XTandemAdapter Annotates MS/MS spectra using X! Tandem. 4
Zip Data Collection Create a zip archive of a data collection. 1
ZIP nmrML Collection Create a zip archive of a nmrML collection. 1