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http://csbg.cnb.csic.es/mbrole/
Software program for overrepresentation (enrichment) analysis of categorical annotations for a set of compounds. These categorical annotations correspond to biological and chemical information found in public databases and software. Annotations can be biological (pathways, enzyme interactions, pharmacological action) or chemical (taxonomy and chemical groups).
Proper citation: MBRole (RRID:SCR_014684) Copy
http://dgrapov.github.io/MetaMapR/
An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.
Proper citation: MetaMapR (RRID:SCR_014685) Copy
A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.
Proper citation: Metscape (RRID:SCR_014687) Copy
http://chenomx.com/software/software.php?pageID=32
A software suite for identifying and quanitfying compounds in NMR spectra. Features include a compound profiler, tools to process data, a compound builder, spin simulator and library manager. More information can be requested, and installation instructions are available on the website.
Proper citation: Chenomx NMR Suite (RRID:SCR_014682) Copy
http://umetrics.com/products/simca
A company that provides data analysis software with features such as multivariate tools, data mining, process modeling and interactive graphics.
Proper citation: SIMCA (RRID:SCR_014688) Copy
https://omictools.com/3omics-tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.
Proper citation: 3Omics (RRID:SCR_014678) Copy
http://cts.fiehnlab.ucdavis.edu
A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services.
Proper citation: Chemical Translation Service (RRID:SCR_014681) Copy
A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide.
Proper citation: NIST Mass Spectrometry Data Center (RRID:SCR_014680) Copy
https://imdevsoftware.wordpress.com/software/
A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis.
Proper citation: DeviumWeb (RRID:SCR_014683) Copy
http://metap.helmholtz-muenchen.de/metap2/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaP (RRID:SCR_014686) Copy
http://www.acdlabs.com/resources/freeware/nmr_proc/
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.
Proper citation: ACD/ NMR Processor (RRID:SCR_014679) Copy
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