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.

Desktop app
Metabolite Automatic… Metabolite Automatic Identification Toolkit

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…

Web app
MetaboAnalyst MetaboAnalyst

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…

Web app
Metabolite Biological… Metabolite Biological Role

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…

Web app
Desktop app
FluxFix FluxFix

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…

Desktop app
MetaNetter MetaNetter

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.…

Desktop app
Marker Visualization Marker Visualization

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…

Desktop app
KMMDA KMMDA

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…

Desktop app
MET-XAlign MET-XAlign

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…

Desktop app
Mathematica package… Mathematica package for Differential Analysis of…

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…

Desktop app
TriDAMP TriDAMP

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…

Web app
MeltDB MeltDB

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…

Web app
EasyLCMS EasyLCMS

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…

Web app
HayStack HayStack

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…

Desktop app
MetAssign MetAssign

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…

Desktop app
MetDisease MetDisease

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.

Desktop app
AStream AStream

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.

Desktop app
CAMERA CAMERA

CAMERA

A package integrating algorithms to extract compound spectra, annotate isotope…

A package integrating 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…

Desktop app
MetScape MetScape

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…

Desktop app
Pathway Activity… Pathway Activity Profiling

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…

Web app
Metabolite Pathway… Metabolite Pathway Enrichment Analysis

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…

Web app
Metabolite Set… Metabolite Set Enrichment Analysis

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…

Desktop app
ProbMetab ProbMetab

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.

Desktop app
MetaMapp MetaMapp

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.

Desktop app
LICRE LICRE

LICRE

An unsupervised feature reduction approach for lipidomic data.

An unsupervised feature reduction approach for lipidomic data.

Web app
Metabolomics Pathway… Deprecated Metabolomics Pathway Analysis

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…

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