Links to Metabolomics Tools

mwTab Parsers

• Python mwtab library for reading and writing files in mwTab format used by the Metabolomics Workbench

R Packages for Statistical Analysis

• MAI(Mechanism-aware imputation) R package which uses a two-step approach to imputing missing data in metabolomics.
  A REST API option is also available.
• MsPrep R package which provides a convenient set of functionalities used in the pre-analytic processing pipeline for MS-based metabolomics data.
• BATMAN R package for estimating metabolite concentrations from Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm
• CTSgetRR interface to CTS
• Hierarchical Clustering
• imDEV Microsoft Excel add-in for multivariate analyses in R which include: clustering, PCA, PLS, correlation network mapping
• Linear Discriminant Analysis
• Metabolomics Univariate and Multivariate Analysis
• Principal Components Analysis
• The R Project for Statistical Computing

Other Metabolomics Tools

• 3Omics web tool for visualizing and rapidly integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data.
• ACD/ NMR Processor Academic Edition Free NMR processing software for academic and non-commercial use only.
• CHEMDATA.NIST.GOV 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).
• Chemical Translation ServiceWeb-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.
• Chenomix NMR Suite
• Cytoscape Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
• DeviumWebLocal or web-based data analysis and visualization tool including: dynamic data visualization, data summaries, statistical analysis, clustering, PCA, PLS, O-PLS
• KEGG 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
• LIPID MAPS toolsMS analysis tools, structure drawing tools, and command line Perl scripts to generate SD files and structure and ontological data for various lipid categories.
• MBrolemetabolite enrichment analysis
• Metaboanalyst Tool suite for metabolomics analysis
• MetaMapRLocal or web-based tool for generating biochemical interaction (KEGG), structural similarity (PubChem Substructure Fingerprints), mass spectral similarity and correlation based networks.
• MetaP Serverautomates data analysis for the processing of metabolomics experiments
• MetPA A web-based metabolomics tool for pathway analysis & visualization
• MetExplore MetExplore 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 http://nar.oxfordjournals.org/content/38/suppl_2/W132
• MetscapeThe 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.
• SAS and SAS JMP SAS on the server is for data cleansing, integration, security and access. Applications in JMP extends access to specific SAS software features, procedures and solutions.
• Simca Multivariate statistical analysis (PCA, PLSDA etc.)
• Statistica tools for statistical analysis of data
• TeachingDemosTutorials, case studies and demonstrations of metabolomic data analyses
• TIBCO Spotfire tools for statistical analysis of data
• TransOmics Informatics Platform for bioinformatics, statistical analysis, and reporting of key results.