WebSpecmine: a website for metabolomics data analysis and mining
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/61824 |
Resumo: | Metabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool’s implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies. |
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WebSpecmine: a website for metabolomics data analysis and miningmetabolomicsstatistical analysisdata miningmetabolite identificationpathway analysisopen-source softwareScience & TechnologyMetabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool’s implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund (ERDF) under the scope of Norte2020—Programa Operacional Regional do Norte. The authors also acknowledge the funding of the project 22231/01/SAICT/2016, “Biodata.pt – Infraestrutura Portuguesa de Dados Biológicos”, funded by FCT and Lisboa 2020/Portugal2020 Partnership Agreement, through the ERDF.info:eu-repo/semantics/publishedVersionMDPI AGUniversidade do MinhoCardoso, SaraAfonso, T.Maraschin, MarceloRocha, Miguel2019-10-102019-10-10T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/61824engCardoso, Sara; Afonso, T.; Maraschin, Marcelo; Rocha, Miguel, WebSpecmine: a website for metabolomics data analysis and mining. Metabolites, 9(10), 237, 20192218-198910.3390/metabo9100237http://www.mdpi.com/journal/metabolitesinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:45:12Zoai:repositorium.sdum.uminho.pt:1822/61824Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:43:00.873183Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
WebSpecmine: a website for metabolomics data analysis and mining |
title |
WebSpecmine: a website for metabolomics data analysis and mining |
spellingShingle |
WebSpecmine: a website for metabolomics data analysis and mining Cardoso, Sara metabolomics statistical analysis data mining metabolite identification pathway analysis open-source software Science & Technology |
title_short |
WebSpecmine: a website for metabolomics data analysis and mining |
title_full |
WebSpecmine: a website for metabolomics data analysis and mining |
title_fullStr |
WebSpecmine: a website for metabolomics data analysis and mining |
title_full_unstemmed |
WebSpecmine: a website for metabolomics data analysis and mining |
title_sort |
WebSpecmine: a website for metabolomics data analysis and mining |
author |
Cardoso, Sara |
author_facet |
Cardoso, Sara Afonso, T. Maraschin, Marcelo Rocha, Miguel |
author_role |
author |
author2 |
Afonso, T. Maraschin, Marcelo Rocha, Miguel |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Cardoso, Sara Afonso, T. Maraschin, Marcelo Rocha, Miguel |
dc.subject.por.fl_str_mv |
metabolomics statistical analysis data mining metabolite identification pathway analysis open-source software Science & Technology |
topic |
metabolomics statistical analysis data mining metabolite identification pathway analysis open-source software Science & Technology |
description |
Metabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool’s implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-10 2019-10-10T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/61824 |
url |
http://hdl.handle.net/1822/61824 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Cardoso, Sara; Afonso, T.; Maraschin, Marcelo; Rocha, Miguel, WebSpecmine: a website for metabolomics data analysis and mining. Metabolites, 9(10), 237, 2019 2218-1989 10.3390/metabo9100237 http://www.mdpi.com/journal/metabolites |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
MDPI AG |
publisher.none.fl_str_mv |
MDPI AG |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799132985324208128 |