The metaRbolomics Toolbox in Bioconductor and beyond

doi:10.3390/metabo9100200

PMID: 31548506DOI: 10.3390/metabo9100200Sep 25, 2019

The metaRbolomics Toolbox in Bioconductor and beyond

Metabolites

Jan StanstrupSteffen Neumann

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Abstract

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunct...Continue Reading

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Apr 22, 2015·Nucleic Acids Research·Jianguo XiaDavid S Wishart

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MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

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May 15, 2015·Bioinformatics·Ron WehrensPaul H C Eilers

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May 24, 2015·Bioinformatics·Astrid Wachter, Tim Beißbarth

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Extending the Dynamic Range in Metabolomics Experiments by Automatic Correction of Peaks Exceeding the Detection Limit

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biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data

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Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

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Aug 31, 2016·Nature Communications·Nir ShahafAsaph Aharoni

eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC/MS-Based Metabolomics

Sep 2, 2016·Analytical Chemistry·Xavier Domingo-AlmenaraOscar Yanes

Clustering analysis of proteins from microbial genomes at multiple levels of resolution

Sep 3, 2016·BMC Bioinformatics·Leonid ZaslavskyTatiana Tatusova

INDEED: Integrated differential expression and differential network analysis of omic data for biomarker discovery

Sep 7, 2016·Methods : a Companion to Methods in Enzymology·Yiming ZuoHabtom W Ressom

A comparison of latent class, K-means, and K-median methods for clustering dichotomous data

Sep 9, 2016·Psychological Methods·Michael J BruscoDouglas Steinley

IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes

Sep 17, 2016·Bioinformatics·Ruggero FerrazzaPietro Franceschi

Large-scale untargeted LC-MS metabolomics data correction using between-batch feature alignment and cluster-based within-batch signal intensity drift correction

Oct 18, 2016·Metabolomics : Official Journal of the Metabolomic Society·Carl BruniusRikard Landberg

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Nov 22, 2016·Journal of Cheminformatics·Yannick Djoumbou FeunangDavid S Wishart

KEGG: new perspectives on genomes, pathways, diseases and drugs

Dec 2, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima

xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data

Dec 16, 2016·Analytical Chemistry·Karan UppalDean P Jones

KODAMA: an R package for knowledge discovery and data mining

Dec 21, 2016·Bioinformatics·Stefano CacciatoreDavid A MacIntyre

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration

Jan 18, 2017·BMC Bioinformatics·Carles Hernandez-FerrerJuan R González

Evaluation and reduction of the analytical uncertainties in GC-MS analysis using a boundary regression model

Jan 22, 2017·Talanta·Miao YuGuibin Jiang

Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration

Feb 1, 2017·PloS One·Kwanjeera WanichthanarakOliver Fiehn

Network Marker Selection for Untargeted LC-MS Metabolomics Data

Feb 9, 2017·Journal of Proteome Research·Qingpo CaiTianwei Yu

msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics

Feb 15, 2017·Analytical Chemistry·Thomas N LawsonWarwick B Dunn

Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics

Feb 22, 2017·Analytical Chemistry·Leslie MyintKasper D Hansen

compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets

Feb 23, 2017·Analytical Chemistry·William M B EdmandsStephen M Rappaport

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Mar 7, 2017·Metabolomics : Official Journal of the Metabolomic Society·D JacobA Moing

Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data

Mar 14, 2017·Journal of Cheminformatics·Martin Loos, Heinz Singer

metaX: a flexible and comprehensive software for processing metabolomics data

Mar 23, 2017·BMC Bioinformatics·Bo WenSiqi Liu

MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Apr 13, 2017·Bioinformatics·Thomas Naake, Emmanuel Gaquerel

Ten simple rules for making research software more robust

Apr 14, 2017·PLoS Computational Biology·Morgan Taschuk, Greg Wilson

Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites

Apr 15, 2017·The Plant Cell·Gerd U BalckeAlain Tissier

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets

May 10, 2017·Bioinformatics·Francesco Del CarratoreRainer Breitling

Exploring micropollutant biotransformation in three freshwater phytoplankton species

May 10, 2017·Environmental Science. Processes & Impacts·Michael A StravsJuliane Hollender

Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra

May 13, 2017·Rapid Communications in Mass Spectrometry : RCM·Carsten JaegerJan Lisec

Review of emerging metabolomic tools and resources: 2015-2016

Jun 18, 2017·Electrophoresis·Biswapriya B MisraDmitry Grapov

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

Jul 12, 2017·BMC Bioinformatics·Jeremy P KoelmelRichard A Yost

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics

Jul 16, 2017·The International Journal of Biochemistry & Cell Biology·Yann GuittonEtienne A Thévenot

MetaboQC: A tool for correcting untargeted metabolomics data with mass spectrometry detection using quality controls

Jul 26, 2017·Talanta·Mónica Calderón-SantiagoFeliciano Priego-Capote

AssayR: A Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses

Aug 30, 2017·Analytical Chemistry·Jimi WillsAndrew J Finch

Navigating freely-available software tools for metabolomics analysis

Sep 12, 2017·Metabolomics : Official Journal of the Metabolomic Society·Rachel SpicerChristoph Steinbeck

MWASTools: an R/bioconductor package for metabolome-wide association studies

Sep 30, 2017·Bioinformatics·Andrea Rodriguez-MartinezMarc-Emmanuel Dumas

proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry

Oct 17, 2017·Bioinformatics·Alexis DelabrièreEtienne A Thévenot

Evaluation of variable selection methods for random forests and omics data sets

Oct 19, 2017·Briefings in Bioinformatics·Frauke DegenhardtSilke Szymczak

xMWAS: a data-driven integration and differential network analysis tool

Oct 27, 2017·Bioinformatics·Karan UppalJonathan Wren

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Nov 1, 2017·Journal of Cheminformatics·Egon L WillighagenChristoph Steinbeck

mixOmics: An R package for 'omics feature selection and multiple data integration

Nov 4, 2017·PLoS Computational Biology·Florian RohartKim-Anh Lê Cao

Chemometric Methods to Quantify 1D and 2D NMR Spectral Differences Among Similar Protein Therapeutics

Nov 8, 2017·AAPS PharmSciTech·Kang ChenDavid A Keire

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Nov 15, 2017·Nucleic Acids Research·Denise N SlenterEgon L Willighagen

HMDB 4.0: the human metabolome database for 2018

Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert

The Reactome Pathway Knowledgebase

Nov 18, 2017·Nucleic Acids Research·Antonio FabregatPeter D'Eustachio

Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses

Dec 2, 2017·Environmental Microbiology·Jie FengXiaoyan Li

Null diffusion-based enrichment for metabolomics data

Dec 7, 2017·PloS One·Sergio Picart-ArmadaAlexandre Perera-Lluna

R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R

Dec 28, 2017·Bioinformatics·Ryne C RamakerSara J Cooper

New tools and resources in metabolomics: 2016-2017

Jan 3, 2018·Electrophoresis·Biswapriya B Misra

polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach

Jan 3, 2018·Bioinformatics·Mengci LiWei Jia

Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data

Jan 14, 2018·Scientific Reports·Runmin WeiYan Ni

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

Feb 1, 2018·PLoS Computational Biology·Runmin WeiWei Jia

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

Feb 23, 2018·Metabolites·Bofei ZhangEwy A Mathé

SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery

Feb 28, 2018·Analytical Chemistry·Haihong ZhaZheng-Jiang Zhu

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

Mar 2, 2018·PLoS Computational Biology·Charlie BeirnaertKris Laukens

IntLIM: integration using linear models of metabolomics and gene expression data

Mar 7, 2018·BMC Bioinformatics·Jalal K SiddiquiEwy A Mathé

KniMet: a pipeline for the processing of chromatography-mass spectrometry metabolomics data

Mar 27, 2018·Metabolomics : Official Journal of the Metabolomic Society·Sonia LiggiJulian L Griffin

PepsNMR for 1 H NMR metabolomic data pre-processing

Apr 8, 2018·Analytica Chimica Acta·Manon MartinBernadette Govaerts

MetaboDiff: an R package for differential metabolomic analysis

May 3, 2018·Bioinformatics·Andreas MockChristel Herold-Mende

Current Challenges in Plant Eco-Metabolomics

May 8, 2018·International Journal of Molecular Sciences·Kristian PetersNicole M van Dam

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

May 12, 2018·Metabolites·Ivana BlaženovićOliver Fiehn

Statistical and Multivariate Analysis of MS-Based Plant Metabolomics Data

May 16, 2018·Methods in Molecular Biology·Carsten Jaeger, Jan Lisec

SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis

May 24, 2018·Bioinformatics·William M B EdmandsStephen M Rappaport

GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies

Jun 8, 2018·PloS One·Meinolf OttensmannJoseph I Hoffman

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets

Jun 22, 2018·Molecular Systems Biology·Ricard ArgelaguetOliver Stegle

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data

Jun 30, 2018·Bioinformatics·Jasmine Chong, Jianguo Xia

MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions

Jul 23, 2018·Bioinformatics·Kieu Trinh DoJan Krumsiek

DLEMMA-MS-Imaging for Identification of Spatially Localized Metabolites and Metabolic Network Map Reconstruction

Aug 1, 2018·Analytical Chemistry·Liron FeldbergAsaph Aharoni

Variable selection and validation in multivariate modelling

Aug 31, 2018·Bioinformatics·Lin ShiCarl Brunius

metaGraphite-a new layer of pathway annotation to get metabolite networks

Sep 6, 2018·Bioinformatics·Gabriele SalesChiara Romualdi

A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data

Sep 13, 2018·Statistical Applications in Genetics and Molecular Biology·Marie Perrot-DockèsGrégory Genta-Jouve

Integrating omics datasets with the OmicsPLS package

Oct 13, 2018·BMC Bioinformatics·Said El BouhaddaniJeanine Houwing-Duistermaat

New approach for understanding genome variations in KEGG

Oct 16, 2018·Nucleic Acids Research·Minoru KanehisaMao Tanabe

The Compound Characteristics Comparison (CCC) approach: a tool for improving confidence in natural compound identification

Oct 24, 2018·Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment·Luca NarduzziPietro Franceschi

KIMBLE: A versatile visual NMR metabolomics workbench in KNIME

Nov 18, 2018·Analytica Chimica Acta·Aswin VerhoevenOleg A Mayboroda

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

Nov 18, 2018·Bioinformatics·Van Du T TranMarco Pagni

MetNet: Metabolite Network Prediction from High-Resolution Mass Spectrometry Data in R Aiding Metabolite Annotation

Dec 1, 2018·Analytical Chemistry·Thomas Naake, Alisdair R Fernie

LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics

Dec 1, 2018·Analytical Chemistry·María Isabel Alcoriza-BalaguerAgustín Lahoz

Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data

Dec 12, 2018·GigaScience·Fadhl M Al-AkwaaLana X Garmire

Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR

Dec 19, 2018·Scientific Reports·Paul HeinrichKatja Dettmer

MetProc: Separating Measurement Artifacts from True Metabolites in an Untargeted Metabolomics Experiment

Dec 19, 2018·Journal of Proteome Research·Mark D ChaffinLiming Liang

CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics

Jan 17, 2019·Bioinformatics·Tobias DepkeMark Brönstrup

Structure/reaction directed analysis for LC-MS based untargeted analysis

Jan 22, 2019·Analytica Chimica Acta·Miao YuJanusz Pawliszyn

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

Jan 29, 2019·Analytical Chemistry·Nils HoffmannAndrew R Jones

Miso: an R package for multiple isotope labeling assisted metabolomics data analysis

Feb 7, 2019·Bioinformatics·Yonghui DongAsaph Aharoni

rDolphin: a GUI R package for proficient automatic profiling of 1D 1 H-NMR spectra of study datasets

Jan 31, 2018·Metabolomics : Official Journal of the Metabolomic Society·Daniel CañuetoNicolau Cañellas

NormalizeMets: assessing, selecting and implementing statistical methods for normalizing metabolomics data

Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Alysha M De LiveraDarren J Creek

Biodiversity Drives Micropollutant Biotransformation in Freshwater Phytoplankton Assemblages

Mar 16, 2019·Environmental Science & Technology·Michael A StravsJuliane Hollender

CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

Mar 25, 2019·Bioinformatics·Oriol SenanMarta Sales-Pardo

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics

Apr 5, 2019·Nature Communications·Xiaotao ShenZheng-Jiang Zhu

omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Apr 13, 2019·Microbiology Resource Announcements·Connor R Tiffany, Andreas J Bäumler

ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra

Apr 13, 2019·Bioinformatics·Gaëlle LefortRémi Servien

NMR Spectroscopy for Metabolomics Research

Jun 30, 2019·Metabolites·Abdul-Hamid EmwasDavid S Wishart

DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics

Aug 23, 2019·Analytical Chemistry·Yandong YinZheng-Jiang Zhu

Citations

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

Mar 9, 2020·Metabolomics : Official Journal of the Metabolomic Society·Keiron O'Shea, Biswapriya B Misra

Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources

May 21, 2020·Metabolites·Tara EicherAnd Ewy A Mathé

Network based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation

May 9, 2020·Expert Review of Proteomics·Leonardo Perez de SouzaAlisdair R Fernie

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

Dec 22, 2019·Metabolites·Julijana Ivanisevic, Elizabeth J Want

Computational Oncology in the Multi-Omics Era: State of the Art

Apr 23, 2020·Frontiers in Oncology·Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus

Struct: an R/bioconductor-based framework for standardised metabolomics data analysis and beyond

Dec 17, 2020·Bioinformatics·Gavin Rhys LloydRalf J M Weber

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