MetaMapR statistics

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Citations per year

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MetaMapR specifications

Information


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
Requirements
Shiny
Maintained Yes

Versioning


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Information


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 in pipelines

 (2)
2018
PMCID: 5797631
PMID: 29440987
DOI: 10.3389/fnins.2018.00032

[…] pathway analysis was carried out using hypergeometric test for enrichment, degree centrality for topology and the gene-metabolite database option. measured metabolite names were used as input for metamapr (grapov et al., ), to build a network that displays structural similarity of metabolites based on their pubchem substructure fingerprints. the network was then exported and visualized using […]

2015
PMCID: 4562606
PMID: 26396492
DOI: 10.4137/BMI.S29511

[…] databases to provide methods for integration and visualization of complex metabolomic results even in cases where biochemical domain knowledge or molecular annotations are unknown. for example, metamapr has been used to integrate both biochemical reaction information with molecular structural and mass spectral similarity to identify pathway-independent relationships, including, […]


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MetaMapR in publications

 (10)
PMCID: 5797631
PMID: 29440987
DOI: 10.3389/fnins.2018.00032

[…] pathway analysis was carried out using hypergeometric test for enrichment, degree centrality for topology and the gene-metabolite database option. measured metabolite names were used as input for metamapr (grapov et al., ), to build a network that displays structural similarity of metabolites based on their pubchem substructure fingerprints. the network was then exported and visualized using […]

PMCID: 5764261
PMID: 29324762
DOI: 10.1371/journal.pone.0190632

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

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 […]


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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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