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

被引：554

作者：

Chong, Jasmine

Xia, Jianguo ^{[1
]}

机构：

[1] McGill Univ, Inst Parasitol, Ste Anne De Bellevue, PQ H9X 3V9, Canada

来源：

BIOINFORMATICS | 2018年 / 34卷 / 24期

基金：

加拿大自然科学与工程研究理事会;

关键词：

D O I：

10.1093/bioinformatics/bty528

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data.

引用

页码：4313 / 4314

页数：2

共 14 条

[1]

[Anonymous], 2016, R LANG ENV STAT COMP

[2] MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis [J].

Chong, Jasmine ;

Soufan, Othman ;

Li, Carin ;

Caraus, Iurie ;

Li, Shuzhao ;

Bourque, Guillaume ;

Wishart, David S. ;

Xia, Jianguo .

NUCLEIC ACIDS RESEARCH, 2018, 46 (W1) :W486-W494

[3] Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data [J].

Davidson, Robert L. ;

Weber, Ralf J. M. ;

Liu, Haoyu ;

Sharma-Oates, Archana ;

Viant, Mark R. .

GIGASCIENCE, 2016, 5

[4]

Gardinassi LG., 2017, Current Pharmacology Reports, V3, P374, DOI [10.1007/s40495-017-0107-0, DOI 10.1007/S40495-017-0107-0]

[5] Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics [J].

Giacomoni, Franck ;

Le Corguille, Gildas ;

Monsoor, Misharl ;

Landi, Marion ;

Pericard, Pierre ;

Petera, Melanie ;

Duperier, Christophe ;

Tremblay-Franco, Marie ;

Martin, Jean-Francois ;

Jacob, Daniel ;

Goulitquer, Sophie ;

Thevenot, Etienne A. ;

Caron, Christophe .

BIOINFORMATICS, 2015, 31 (09) :1493-1495

[6] The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience [J].

Griss, Johannes ;

Jones, Andrew R. ;

Sachsenberg, Timo ;

Walzer, Mathias ;

Gatto, Laurent ;

Hartler, Juergen ;

Thallinger, Gerhard G. ;

Salek, Reza M. ;

Steinbeck, Christoph ;

Neuhauser, Nadin ;

Cox, Juergen ;

Neumann, Steffen ;

Fan, Jun ;

Reisinger, Florian ;

Xu, Qing-Wei ;

del Toro, Noemi ;

Perez-Riverol, Yasset ;

Ghali, Fawaz ;

Bandeira, Nuno ;

Xenarios, Ioannis ;

Kohlbacher, Oliver ;

Vizcaino, Juan Antonio ;

Hermjakob, Henning .

MOLECULAR & CELLULAR PROTEOMICS, 2014, 13 (10) :2765-2775

[7] Systems biology guided by XCMS Online metabolomics [J].

Huan, Tao ;

Forsberg, Erica M. ;

Rinehart, Duane ;

Johnson, Caroline H. ;

Ivanisevic, Julijana ;

Benton, H. Paul ;

Fang, Mingliang ;

Aisporna, Aries ;

Hilmers, Brian ;

Poole, Farris L. ;

Thorgersen, Michael P. ;

Adams, Michael W. W. ;

Krantz, Gregory ;

Fields, Matthew W. ;

Robbins, Paul D. ;

Niedernhofer, Laura J. ;

Ideker, Trey ;

Majumder, Erica L. ;

Wall, Judy D. ;

Rattray, Nicholas J. W. ;

Goodacre, Royston ;

Lairson, Luke L. ;

Siuzdak, Gary .

NATURE METHODS, 2017, 14 (05) :461-462

[8] Building Predictive Models in R Using the caret Package [J].

Kuhn, Max .

JOURNAL OF STATISTICAL SOFTWARE, 2008, 28 (05) :1-26

[9]

Leisch F, 2002, COMPSTAT 2002: PROCEEDINGS IN COMPUTATIONAL STATISTICS, P575

[10] Predicting Network Activity from High Throughput Metabolomics [J].

Li, Shuzhao ;

Park, Youngja ;

Duraisingham, Sai ;

Strobel, Frederick H. ;

Khan, Nooruddin ;

Soltow, Quinlyn A. ;

Jones, Dean P. ;

Pulendran, Bali .

PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (07)

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