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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

http://www.universityofcalifornia.edu/

Public research university system in the U.S. state of California with campuses at Berkeley, Davis, Irvine, Los Angeles, Merced, Riverside, San Diego, San Francisco, Santa Barbara, and Santa Cruz, along with numerous research centers and academic abroad centers.

Proper citation: University of California; California; USA (RRID:SCR_011617) Copy   

•   Source: SciCrunch Registry

https://www.niddk.nih.gov/

Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.

Proper citation: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) Copy   

•   Source: SciCrunch Registry

http://www.cosmos-fp7.eu

A group which aims to create open standards for metabolomics data shsaring and analysis.

Proper citation: Coordination of Standards in Metabolomics (RRID:SCR_014662) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.bml-nmr.org

A collection of experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards.

Proper citation: Birmingham Metabolite Library (RRID:SCR_014666) Copy   

•   Source: SciCrunch Registry

http://jcggdb.jp/rcmg/glycodb/Ms_ResultSearch

A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans.

Proper citation: Glycan Mass Spectral Database (GMDB) (RRID:SCR_014667) Copy   

•   Source: SciCrunch Registry

https://www.nist.gov/srd/nist-standard-reference-database-1a-v14

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Proper citation: Mass Spectral Library (RRID:SCR_014668) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://imdevsoftware.wordpress.com/tutorials/

A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals.

Proper citation: TeachingDemos (RRID:SCR_014689) 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

http://www.jmp.com/en_us/software/jmp.html

Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design.

Proper citation: JMP (RRID:SCR_014242) 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

https://imdevsoftware.wordpress.com/imdev/

A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.

Proper citation: imDEV (RRID:SCR_014674) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry