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Interpretation (MS-based metabolomic analysis)

One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data, and incorporate prior knowledge of pathways and molecular interactions.

MetaboAnalyst
Web

MetaboAnalyst

Provides a user-friendly, web-based analytical pipeline for high-throughput…

Provides a user-friendly, web-based analytical pipeline for high-throughput metabolomics studies. In particular, MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data…

CAMERA
Desktop

CAMERA

Integrates algorithms to extract compound spectra, annotate isotope and adduct…

Integrates algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. CAMERA integrates multiple methods for…

MetScape
Desktop

MetScape

Provides a bioinformatics framework for the visualization and interpretation of…

Provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism. MetScape allows users to build and…

MSEA
Web

MSEA Metabolite Set Enrichment Analysis

A web-based tool to help identify and interpret patterns of metabolite…

A web-based tool to help identify and interpret patterns of metabolite concentration changes in a biologically meaningful context for human and mammalian metabolomic studies. Key to the development…

PAPi
Desktop

PAPi Pathway Activity Profiling

Compares metabolic pathway activities from metabolite profiles. The PAPi…

Compares metabolic pathway activities from metabolite profiles. The PAPi package allows to quickly compare metabolic pathways activities between different experimental conditions. Using the…

MAIT
Desktop

MAIT Metabolite Automatic Identification Toolkit

An R package of a set of tools and functions to perform an automatic end-to-end…

An R package of a set of tools and functions to perform an automatic end-to-end analysis of LC/MS metabolomic data, putting special emphasis on peak annotation and metabolite identification. The goal…

MPEA
Web

MPEA Metabolite Pathway Enrichment Analysis

A rapid tool for functional analysis and biological interpretation of metabolic…

A rapid tool for functional analysis and biological interpretation of metabolic profiling data. MPEA follows the concept of gene set enrichment analysis (GSEA) and tests whether metabolites involved…

MetDisease
Desktop

MetDisease

This framework can be used to infer connections between metabolites and…

This framework can be used to infer connections between metabolites and diseases through annotated disease genes.

ProbMetab
Desktop

ProbMetab

An R package that promotes substantial improvement in automatic probabilistic…

An R package that promotes substantial improvement in automatic probabilistic liquid chromatography-mass spectrometry-based metabolome annotation.

MetaMapp
Desktop

MetaMapp

A tool to construct metabolomics network graphs from the chemical similarity…

A tool to construct metabolomics network graphs from the chemical similarity and mass spectral similarity matrices and the KEGG reaction pair database.

MarVis-Suite
Desktop

MarVis-Suite Marker Visualization

A toolbox for interactive ranking, filtering, combination, clustering,…

A toolbox for interactive ranking, filtering, combination, clustering, visualization, and functional analysis of data sets containing intensity-based profile vectors (data set features or marker…

MetCirc
Desktop

MetCirc

Aligns and calculates pairwise similarity scores among mass spectrometry…

Aligns and calculates pairwise similarity scores among mass spectrometry (MS)/MS spectral data. MetCirc is an open-source package to make biological sense of mass spectral similarities from…

MET-XAlign
Desktop

MET-XAlign

A metabolite-based alignment approach entitled MET-XAlign to align metabolites…

A metabolite-based alignment approach entitled MET-XAlign to align metabolites across LC/MS metabolomics profiles. MET-XAlign takes the deduced molecular mass and estimated compound retention time…

FluxFix
Web
Desktop

FluxFix

Transforms signal intensity values into percent mole enrichment for each…

Transforms signal intensity values into percent mole enrichment for each isotopologue measured. FluxFix is a web-based calculator that converts raw mass spec AUC values into the percent…

MetAssign
Desktop

MetAssign

Combines information from the mass-to-charge ratio, retention time and…

Combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak…

KMMDA
Desktop

KMMDA

A kernel-based score test for the metabolomics differential expression…

A kernel-based score test for the metabolomics differential expression analysis. In order to simultaneously capture both the continuous pattern and discrete pattern in metabolomics data, two new…

MBRole
Web

MBRole Metabolite Biological Role

Performs overrepresentation (enrichment) analysis of categorical annotations…

Performs overrepresentation (enrichment) analysis of categorical annotations for a set of compounds of interest. These categorical annotations correspond to biological and chemical information…

MetaNetter
Desktop

MetaNetter

A Cytoscape plugin dedicated to the inference and visualization of…

A Cytoscape plugin dedicated to the inference and visualization of high-resolution mass spectrometry data sets. The inference is achieved using a defined list of putative biochemical transformations.…

MeltDB
Web

MeltDB

A next-generation web application addressing storage, sharing, standardization,…

A next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments. New features improve both efficiency and effectivity of the…

HayStack
Web

HayStack

An online tool for rapid processing and analysis of LCMS-based metabolomics…

An online tool for rapid processing and analysis of LCMS-based metabolomics data. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data…

MathDAMP
Desktop

MathDAMP Mathematica package for Differential Analysis of Metabolite Profiles

Facilitates the visualization of differences between metabolite profiles…

Facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all…

TriDAMP
Desktop

TriDAMP

A MathDAMP extension for the visualization of three-way comparisons between…

A MathDAMP extension for the visualization of three-way comparisons between metabolite profiles. TriDAMP is based on the HSB (hue, saturation, brightness) color model. The three compared values are…

AStream
Desktop

AStream

An R-statistical software package for the curation and identification of…

An R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data.

LICRE
Desktop

LICRE

Reduces the number of highly correlated lipid species in a lipidomic dataset…

Reduces the number of highly correlated lipid species in a lipidomic dataset without the need for sample class information. LICRE is an unsupervised feature reduction approach that allows the reduced…

MetPA
Web

MetPA Metabolomics Pathway Analysis

A full-featured, easy-to-use pathway analysis and visualization environment…

A full-featured, easy-to-use pathway analysis and visualization environment that combines advanced statistical enrichment analysis with pathway topological characteristics to help researchers…

EasyLCMS
Web

EasyLCMS

A web application designed to quantify numerous metabolites, simultaneously…

A web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which…

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