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http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry

http://www.metabolomicsworkbench.org/data/metabolitedatabase.php

A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass.

Proper citation: Metabolomics Workbench Metabolite Database (RRID:SCR_014633) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrapov/CTSgetR

R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers.

Proper citation: CTSgetR (RRID:SCR_014672) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://metscape.ncibi.org

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   

•   Source: SciCrunch Registry

http://metabolomicssociety.org

An independent, non-profit organization whose main goal is to promote the growth and development of the field of metabolomics internationally. They also aim to provide collaborative opportunities among scientists in metabolomics, create connections between academia, government and industry in the field of metabolomics, provide opportunities for presentation of research achievements and creation of workshops, and promote the publication of meritorious research in the field.

Proper citation: Metabolomics Society (RRID:SCR_014665) Copy   

•   Source: SciCrunch Registry

http://www.metabolomexchange.org/site/

International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information.

Proper citation: MetabolomeXchange (RRID:SCR_014664) Copy   

•   Source: SciCrunch Registry

https://github.com/stanstrup/mwtabR

An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists.

Proper citation: mwtabR (RRID:SCR_014677) Copy   

•   Source: SciCrunch Registry

https://www.mzcloud.org

A mass spectral database that assists in identifying compunds in life sciences, matabolomics, pharmaceutical research, toxicology, forensic investigations, environemnta analysis, food control, and industry.

Proper citation: mzCloud (RRID:SCR_014669) Copy   

•   Source: SciCrunch Registry

https://www.metabolome-express.org

A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management.

Proper citation: MetabolomeExpress (RRID:SCR_014670) Copy   

•   Source: SciCrunch Registry

http://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

A mass spectral database for organic compounds. The spectra included in the database are: electron impact Mass spectrum (EI-MS), Fourier transform infrared spectrum (FT-IR), 1H nuclear magnetic resonance (NMR) spectrum, 13C NMR spectrum, laser Raman spectrum, and electron spin resonance (ESR) spectrum.

Proper citation: Spectral Database System (SDBS) (RRID:SCR_014671) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metacore/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression.

Proper citation: MetaCore (RRID:SCR_008125) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metabolights/

A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments.

Proper citation: MetaboLights (RRID:SCR_014663) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html

R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.

Proper citation: Hierarchical Clustering (RRID:SCR_014673) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html

R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.

Proper citation: Principal Components Analysis (RRID:SCR_014676) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-devel/library/MASS/html/lda.html

R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular.

Proper citation: Linear Discriminant Analysis (RRID:SCR_014675) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry