Software tools, databases and resources in metabolomics: updates from 2018 to 2019

Metabolomics : Official Journal of the Metabolomic Society
Keiron O'Shea, Biswapriya B Misra

Abstract

Metabolomics has evolved as a discipline from a discovery and functional genomics tool, and is now a cornerstone in the era of big data-driven precision medicine. Sample preparation strategies and analytical technologies have seen enormous growth, and keeping pace with data analytics is challenging, to say the least. This review introduces and briefly presents around 100 metabolomics software resources, tools, databases, and other utilities that have surfaced or have improved in 2019. Table 1 provides the computational dependencies of the tools, categorizes the resources based on utility and ease of use, and provides hyperlinks to webpages where the tools can be downloaded or used. This review intends to keep the community of metabolomics researchers up to date with all the software tools, resources, and databases developed in 2019, in one place.

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Citations

Apr 18, 2020·Analytical and Bioanalytical Chemistry·Dörte Solle
Aug 21, 2020·PLoS Pathogens·Philipp BrandtSlavena Vylkova
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May 19, 2020·Metabolomics : Official Journal of the Metabolomic Society·Mohammad Khodadadi, Morteza Pourfarzam
Sep 24, 2020·International Journal of Molecular Sciences·Aneta BalcerczykGilles J P Rautureau
May 21, 2020·Metabolites·Shruti Pavagadhi, Sanjay Swarup
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Jan 24, 2021·Nature Protocols·Erica L-W MajumderGary Siuzdak
Jan 21, 2021·Analytical Chemistry·Hui-Yin ChangJamey D Young
Jan 21, 2021·Metabolites·Santosh LamichhaneMatej Orešič
Mar 6, 2021·Cell Stem Cell·Cesar A Perez-Ramirez, Heather R Christofk
May 13, 2021·Metabolomics : Official Journal of the Metabolomic Society·Biswapriya B Misra
Jun 7, 2021·Metabolomics : Official Journal of the Metabolomic Society·Jennifer E KyleBobbie-Jo M Webb-Robertson
Jul 3, 2021·Metabolites·Steven LichtenbergPetr G Lokhov
Nov 13, 2020·Analytical Chemistry·Arthur S EdisonSicong Zhang
Sep 3, 2021·Briefings in Bioinformatics·Mohammad Reza KarimiUlf Schmitz

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Methods Mentioned

BETA
NMR
electrophoresis
dissection
phosphotransferase

Software Mentioned

Pixel
Miodin ( MultI - Omics Data INtegration
CLARITE ( CLeaning to Analysis Interface
MetDNA
BiG
macOS X
MASST ( Mass Spectrometry Search Tool )
CFM
FBMN
GitLab

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