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Metabolomics Info

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Tools

  1. metabolomics.info
    Name Metabolomics Info
    Description A service of the Metabolomics Consortium Coordinating Center (M3C) of
    the NIH Common Fund Metabolomics Program.Website and People Portal.
    URL https://metabolomics.info
    Authors
            Name Kevin Hanson
            Email kshanson@ufl.edu
            Name Christopher Barnes
            Email cpb@ufl.edu
            Name Michael Conlon
            Email mconlon@ufl.edu
            Name Taeber Rapczak
            Email taeber@ufl.edu
            Name Hunter Jarrell
            Email hunter.jarrell@ufl.edu
            Name Samantha Emerson
            Email s.emerson@ufl.edu
            Name Alyssa Kelly
            Email alyssakelly@ufl.edu
            Name Jenny Martinez
            Email jmjenny@ufl.edu
            Name Naomi Braun
            Email looseymoose@ufl.edu
    Tags
    service

  2. github.com/MoseleyBioinformaticsLab/mwtab
    Name mwtab
    Description Parser for mwtab files from the Metabolomics Workbench.
    URL https://github.com/MoseleyBioinformaticsLab/mwtab
    Authors
            Name Andrey Smelter
            Email andrey.smelter@gmail.com
    License   
            Kind BSD 3-Clause Clear License
            URL https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/LICENSE
    Tags
    python
    mwtab

  3. batman.r-forge.r-project.org
    Name Bayesian AuTomated Metabolite Analyser for NMR spectra
    Description BATMAN is an R package for estimating metabolite concentrations from Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm.
    URL http://batman.r-forge.r-project.org/
    Authors
            Name Jie Hao
            Email j.hao@ic.ac.uk
            Name William Astle
            Email william.astle@mail.mcgill.ca
            Name Maria De Iorio
            Email m.deiorio@ucl.ac.uk
            Name Timothy Ebbels
            Email t.ebbels@ic.ac.uk
    License   
            Kind Boost Software License Version 1.0
            URL https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/batman/LICENSE_1_0.txt?root=batman
    Tags
    r

  4. github.com/dgrapov/CTSgetR
    Name CTSgetR
    Description "R interface to Chemical Translation Service (CTS)"
    URL https://github.com/dgrapov/CTSgetR
    Authors
            Name Dmitry Grapov
            Email dgrapov@gmail.com
    License   
            Kind MIT
            URL https://opensource.org/licenses/MIT
    Tags
    r

  5. stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html
    Name Hierarchical Clustering
    Description "Hierarchical cluster analysis on a set of dissimilarities and methods for analyzing it."
    URL https://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html
    Authors
            Name Fionn Murtagh
            Email fmurtagh@acm.org
    License   
            Kind GNU GENERAL PUBLIC LICENSE
            URL https://cran.r-project.org/web/licenses/GPL-3
    Tags
    r

  6. stat.ethz.ch/R-manual/R-devel/library/MASS/html/lda.html
    Name Linear Discriminant Analysis
    Description "Linear discriminant analysis."
    URL https://stat.ethz.ch/R-manual/R-devel/library/MASS/html/lda.html
    Authors None
    License   
            Kind GNU General Public License
            URL https://www.r-project.org/Licenses/GPL-2
    Tags
    r

  7. cran.r-project.org/web/packages/muma/index.html
    Name Metabolomics Univariate and Multivariate Analysis
    Description "Preprocessing of high-throughput data (normalization and scalings)"
    URL https://cran.r-project.org/web/packages/muma/index.html
    Authors
            Name Edoardo Gaude
            Email egaude541@gmail.com
            Name Francesca Chignola
            Name Dimitrios Spiliotopoulos
            Name Silvia Mari
            Name Andrea Spitaleri
            Name Michela Ghitti
    License   
            Kind GNU GENERAL PUBLIC LICENSE
            URL https://cran.r-project.org/web/licenses/GPL-3
    Tags
    r

  8. stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html
    Name Principal Components Analysis
    Description "Performs a principal components analysis on the given data matrix and returns the results as an object of class prcomp."
    URL https://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html
    License   
            Kind GNU General Public License
            URL https://www.r-project.org/Licenses/GPL-2
    Tags
    r

  9. cran.cnr.berkeley.edu/
    Name The Comprehensive R Archive Network
    Description "freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques."
    URL http://cran.cnr.berkeley.edu/
    License   
            Kind GNU GENERAL PUBLIC LICENSE
            URL https://www.r-project.org/Licenses/GPL-2
    Tags
    r

  10. 3omics.cmdm.tw
    Name 3omics
    Description "Web tool for visualizing and rapidly integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data."
    URL https://3omics.cmdm.tw
    Tags
    service

  11. acdlabs.com/products/adh/spectrusprocessor/index.php
    Name ACD/ NMR Processor Academic Edition
    Description "Free NMR processing software for academic and non-commercial use only"
    URL https://www.acdlabs.com/products/adh/spectrusprocessor/index.php
    Tags
    service

  12. CHEMDATA.NIST.GOV
    Name Mass Spectrometry Data Center
    Description "Mass spectral libraries and data analysis tools include AMDIS (Automated Mass Spectral Deconvolution and Identification System for GC/MS) and MS Interpreter (for fragmentation analysis)."
    URL https://chemdata.nist.gov
    Tags
    database

  13. cts.fiehnlab.ucdavis.edu/
    Name Chemical Translation Service
    Description "Web-based service for metabolite identifier translation between > 200 common biological databases, including; Chemical Name, InChIKey, PubChem, ChemSpider, BioCyc, ChEBI, CAS, HMDB, KEGG and LIPID MAPS."
    URL http://cts.fiehnlab.ucdavis.edu/
    Authors
            Name Sajjan Mehta
            Name Diego Pedrosa
    License   
            Kind GNU LESSER GENERAL PUBLIC LICENSE
            URL http://www.gnu.org/licenses/lgpl-3.0.html
    Tags
    angularJS

  14. chenomx.com
    Name Chenomx NMR Suite
    Description "Chenomx specializes in mixture analysis for applications in life sciences such as metabolomics, food/nutrition, and cell culture research."
    URL https://www.chenomx.com
    Tags
    service

  15. cytoscape.org
    Name Cytoscape
    Description "Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data"
    URL https://cytoscape.org
    License   
            Kind GNU LESSER GENERAL PUBLIC LICENSE
            URL http://www.gnu.org/licenses/lgpl-3.0.html
    Tags
    r

  16. github.com/dgrapov/DeviumWeb
    Name DeviumWeb
    Description "Interactive multivariate data analysis in R implemented in shiny."
    URL https://github.com/dgrapov/DeviumWeb
    Authors
            Name Dmitry Grapov
            Email dgrapov@gmail.com
    License   
            Kind AGPLv3
            URL http://www.tldrlegal.com/l/AGPL3
    Tags
    r

  17. genome.jp/kegg/
    Name Kyoto Encyclopedia of Genes and Genomes
    Description "KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies"
    URL https://www.genome.jp/kegg/
    License   
            Kind Multiple
            URL https://www.kegg.jp/kegg/legal.html
    Tags
    database

  18. csbg.cnb.csic.es/mbrole2/
    Name MBrole 2.0
    Description 'Metabolite enrichment analysis'
    URL http://csbg.cnb.csic.es/mbrole2/
    Authors
            Name Javier Lopez-Lbanez
            Email jlopezibanez@cnb.csic.es
    License   
            Kind Creative Commons Attribution-NonCommercial 4.0 International License
            URL https://creativecommons.org/licenses/by-nc/4.0/
    Tags
    database

  19. github.com/dgrapov/MetaMapR
    Name MetaMapR
    Description "Local or web-based tool for generating biochemical interaction (KEGG), structural similarity (PubChem Substructure Fingerprints), mass spectral similarity and correlation based networks."
    URL http://dgrapov.github.io/MetaMapR/
    Authors
            Name Dmitry Grapov
            Email dgrapov@gmail.com
    License   
            Kind GNU General Public License
            URL https://github.com/dgrapov/MetaMapR/blob/master/LICENSE
    Tags
    html
    css
    javascrip

  20. metap.helmholtz-muenchen.de/metap2
    Name metaP-server
    Description "Automates data analysis for the processing of metabolomics experiments."
    URL http://metap.helmholtz-muenchen.de/metap2/
    Authors
            Name Gabi Kastenmüller
            Email presse@helmholtz-muenchen.de
            Name Werner Römisch-Margl
    License   
            Kind Multiple
            URL https://www.pathway.jp/licensing/commercial.html
    Tags
    service

  21. metexplore.fr
    Name MetaExplore
    Description "MetaExplore is a free academic service allowing; Importing/storing/sharing
    genome scale metabolic networks; Mapping polyomics data;
    Pathway enrichment; Visualizing networks; Mining networks based on data and
    network structure; and Computing fluxes"
    URL http://www.metexplore.fr
    Authors
            Name Institut national de la recherche agronomique
    License   
            Kind Creative Commons Attribution-NonCommercial 4.0 International License.
            URL https://creativecommons.org/licenses/by-nc/4.0/
    Tags
    service

  22. metscape.ncibi.org/
    Name MetScape 3 for Cytoscape
    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."
    URL http://metscape.ncibi.org/
    Authors
            Name Bill Duren
            Email metscape-help@umich.edu
            Name Terry E. Weymouth
            Name Tim Hull
            Name Alla Karnovsky
    Tags
    plugin

  23. umetrics.com/products/simca
    Name SIMCA
    Description "Multivariate statistical analysis (PCA, PLSDA etc.)"
    URL https://umetrics.com/products/simca
    Authors
            Name Sartorius Stedim Biotech
            Email umetrics@sartorius-stedim.com
    Tags
    application

  24. statsoft.com/Products/STATISTICA-Features
    Name Statistica product features
    Description "Tools for statistical analysis of data"
    URL http://www.statsoft.com/Products/STATISTICA-Features
    Tags
    visual basic
    r

  25. imdevsoftware.wordpress.com/tutorials/
    Name Teaching Demos
    Description "DemosTutorials, case studies and demonstrations of metabolomic data analyses"
    URL https://imdevsoftware.wordpress.com/tutorials/
    Authors
            Name Dmitry Grapov
            Email dgrapov@gmail.com
    License   
            Kind Creative Commons Attribution-NonCommercial 4.0 International License.
            URL https://creativecommons.org/licenses/by-nc/4.0/
    Tags
    tutorial

  26. tibco.com/products/tibco-spotfire
    Name Tibco Spotfire
    Description "Tools for statistical analysis of data."
    URL https://www.tibco.com/products/tibco-spotfire
    Authors None
    Tags
    service

  27. waters.com/waters/library.htm?lid=134683264&locale=en_US
    Name TransOmics Informatics Powered by Nonlinear Dynamics
    Description "Platform for bioinformatics, statistical analysis, and reporting of key results."
    URL https://www.waters.com/waters/library.htm?lid=134683264&locale=en_US
    Authors
            Name Lee Gethings
            Name Martha Stapels
            Name Ian Mons
            Name Jackson Pope
            Name James Langridge
    Tags
    documentation

Most of the data is from the Metabolomics Tools Wiki .