MetaMapR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MetaMapR

Tool usage distribution map

This map represents all the scientific publications referring to MetaMapR per scientific context
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Associated diseases

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MetaMapR specifications


Unique identifier OMICS_07956
Name MetaMapR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Maintained Yes


No version available


Unique identifier OMICS_07956
Name MetaMapR
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Version 1.4.0
Stability Stable
Maintained Yes

Publication for MetaMapR

MetaMapR citations


When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors

PMCID: 5876533
PMID: 29495643
DOI: 10.3390/ht7010007

[…] lites, genes, and pathways in order to display them in the context of metabolic networks. In addition, there are platform independent online tools available, such as ProMeTra [] and Paintomics [], or MetaMapR []; the latter is an association-based analysis and visualization tool that leverages the KEGG and PubChem databases to also integrate unknowns in given analyses.As the final step in the anal […]


Obesogenic diets alter metabolism in mice

PLoS One
PMCID: 5764261
PMID: 29324762
DOI: 10.1371/journal.pone.0190632
call_split See protocol

[…] FDR correction and post hoc testing. PCA analysis was used for multivariate statistics and visualization. For network mapping, KEGG reactant pairs and Tanimoto similarity calculations were done using MetaMapR []. Networks were then created using Cytoscape []. Chemical enrichment calculations were done using ChemRICH []. […]


Computational dynamic approaches for temporal omics data with applications to systems medicine

BioData Min
PMCID: 5473988
PMID: 28638442
DOI: 10.1186/s13040-017-0140-x

[…] on II. More importantly, those packages can incorporate the correlation analysis with other types of relationships such as biochemical reactions and molecular structural and mass spectral similarity (MetaMapR).In addition, they provide a dynamic interface (Grinn) to integrate gene, protein, and metabolite data using more advanced biological-network-based approaches such as Gaussian graphical model […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] uild the networks, which can also improve annotation of unknown compounds. MetaNetter [] uses raw high-resolution data and a list of potential biochemical transformations to infer metabolic networks. MetaMapR [] builds chemical and spectral similarity networks based on annotated and unknown compounds. ChemTreeMap [] uses annotated structures and a computational approach to produce hierarchical tre […]


The metabolomics of psoriatic disease

PMCID: 5562362
PMID: 28824870
DOI: 10.2147/PTT.S118348

[…] meaningful way, it must then be mapped onto metabolic pathway databases, such as the Kyoto Encyclopedia of Genes and Genomes. This requires sophisticated statistical tools, such as MetaboAnalyst and MetaMapR, to perform pathway and network analyses.Sample analysis involves the separation of the mixture into its biochemical constituents followed by the identification and quantification of each com […]


Computational approaches in target identification and drug discovery

Comput Struct Biotechnol J
PMCID: 4887558
PMID: 27293534
DOI: 10.1016/j.csbj.2016.04.004

[…] bstitution or indel has an impact on the biological function of a protein and GenePattern provides with analytical tools for the analysis of gene expression, sequence variation and network analysis. MetaMapR, an open source software integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networ […]

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MetaMapR institution(s)
National Institutes of Health West Coast Metabolomics Center; Genome Center, University of California Davis, Davis CA, USA

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