PIUMet – Network Integration of Untargeted Metabolomics

PIUMet

:: DESCRIPTION

PIUMet is a network-based algorithm for integrative analysis of untargeted metabolomic data. It leverages known metabolic reactions and protein-protein interactions to analyze the ambiguous assignment of metabolomics features and identify disease-associated pathways and hidden components.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E.
Revealing disease-associated pathways by network integration of untargeted metabolomics.
Nat Methods. 2016 Sep;13(9):770-6. doi: 10.1038/nmeth.3940. Epub 2016 Aug 1. PMID: 27479327; PMCID: PMC5209295.

MetaClean 1.0.0 – Detection of Low-Quality Peaks in Untargeted Metabolomics Data

MetaClean 1.0.0

:: DESCRIPTION

MetaClean is a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data

::DEVELOPER

Jan Krumsiek lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

MetaClean

:: MORE INFORMATION

Citation

Chetnik K, Petrick L, Pandey G.
MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data.
Metabolomics. 2020 Oct 21;16(11):117. doi: 10.1007/s11306-020-01738-3. PMID: 33085002; PMCID: PMC7895495.

maplet 1.1.1 – Metabolomics Analysis PipeLinE Toolbox

maplet 1.1.1

:: DESCRIPTION

maplet is an R package for statistical data analysis with a special focus on metabolomics datasets. It allows users to create self-contained analytical pipelines.

::DEVELOPER

Jan Krumsiek lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

maplet

:: MORE INFORMATION

Citation

Chetnik K, Benedetti E, Gomari DP, Schweickart A, Batra R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek J.
maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines.
Bioinformatics. 2021 Oct 25:btab741. doi: 10.1093/bioinformatics/btab741. Epub ahead of print. PMID: 34694386.

MET-IDEA 2.08 – Data Extraction Tool for Mass Spectrometry-based Metabolomics

MET-IDEA 2.08

:: DESCRIPTION

MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semi-quantitative data from raw data files, which allows for more rapid biological insight.

::DEVELOPER

Sumner Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MET-IDEA

:: MORE INFORMATION

Citation

Broeckling CD, Reddy IR, Duran AL,Zhao X and Sumner LW.
MET-IDEA: data extraction tool for mass spectrometry-based metabolomics.
Anal Chem. 2006 Jul 1;78(13):4334-41.

COVAIN 20170509 – Multivariate Statistical Analysis of Metabolomics Covariance data

COVAIN 20170509

:: DESCRIPTION

COVAIN (Covariance Inverse ) is a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data.

::DEVELOPER

Molecular Systems Biology, University of Vienna

:: SCREENSHOTS

COVAIN

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 COVAIN

:: MORE INFORMATION

Citation:

COVAIN: A toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data.
Xiaoliang Sun and Wolfram Weckwerth
Metabolomics. Volume 8, 2012.

metabnorm 20141112 – A mixed model Normalization method for Metabolomics data

metabnorm 20141112

:: DESCRIPTION

metabnorm is a mixed model normalization method for metabolomics data

::DEVELOPER

Alexandra Jauhiainen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

 metabnorm

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2.
Normalization of metabolomics data with applications to correlation maps.
Jauhiainen A1, Basetti M, Narita M, Narita M, Griffiths J, Tavaré S.

metaP 2 – web-based Metabolomics data analysis tool

metaP 2

:: DESCRIPTION

The metaP server automates data analysis for the processing of metabolomics experiments.

::DEVELOPER

Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomed Biotechnol. 2011;2011. pii: 839862. doi: 10.1155/2011/839862. Epub 2010 Sep 5.
metaP-server: a web-based metabolomics data analysis tool.
Kastenmüller G1, Römisch-Margl W, Wägele B, Altmaier E, Suhre K.

mzMatch/PeakML 2.0 – Metabolomics Data Analysis

mzMatch/PeakML 2.0

:: DESCRIPTION

mzMatch is a modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data. The mzMatch environment was based entirely on the PeakML file format and core library, which provides a common framework for all the tools.

::DEVELOPER

mzMatch team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java/ R

:: DOWNLOAD

 mzMatch/PeakML

:: MORE INFORMATION

Citation

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.
Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R.
Anal Chem. 2011 Apr 1;83(7):2786-93. doi: 10.1021/ac2000994

MIDAS 1.1 – A Database-Searching Algorithm for Metabolite Identification in Metabolomics

MIDAS 1.1

:: DESCRIPTION

MIDAS (Metabolite Identification via Database Searching) is a database searching approach which can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database.

::DEVELOPER

the Pan lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

 MIDAS

:: MORE INFORMATION

Citation

Anal Chem. 2014 Sep 11.
MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics.
Wang Y1, Kora G, Bowen BP, Pan C.

MetScape 3.1.3 – Analysis and Visualization of Metabolomics and Gene Expression data

MetScape 3.1.3

:: DESCRIPTION

The MetScape Plugin for Cytoscape provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism.

::DEVELOPER

MetScape team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 MetScape

:: MORE INFORMATION

Citation

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.
Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS.
Bioinformatics. 2012 Feb 1;28(3):373-80. doi: 10.1093/bioinformatics/btr661.

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