ProbMetab specifications

Information


Unique identifier OMICS_02407
Name ProbMetab
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ProbMetab

ProbMetab citations

 (2)
library_books

Navigating freely available software tools for metabolomics analysis

2017
Metabolomics
PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] t et al. ), KEGG (Kanehisa et al. ), LMSD (Sud et al. ), BioCyc (Caspi et al. ) and DrugBank (Wishart et al. ) is then used for putative annotation.Implemented in R, both MetAssign (Daly et al. ) and ProbMetab (Silva et al. ) use Bayesian approaches to putatively annotate peaks. MetAssign is a probabilistic putative metabolite identification algorithm, implemented in mzMatch (Scheltema et al. ) th […]

library_books

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

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] samples to build networks that can be visualized in PDF or exported to Cytoscape. This can be a very useful approach to identify related compounds and associate them to metabolic pathways. Similarly, ProbMetab [] is an R package for probabilistic annotation of compounds based on the method developed by Rogers et al. (2009) [] that incorporates information on possible biochemical reactions between […]

ProbMetab institution(s)
LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil; INRA UMR1331, Toxalim, Research Centre in Food Toxicology, Universit de Toulouse, INSA, UPS, INP

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