Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis

Detalhes bibliográficos
Autor(a) principal: Palu, Cintia C.
Data de Publicação: 2019
Outros Autores: Ribeiro-Alves, Marcelo, Wu, Yanxin, Lawlor, Brendan, Baranov, Pavel V., Kelly, Brian, Walsh, Paul
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/60259
Resumo: This work was supported by the grants from the Irish Research Council Enterprise Partnership; the SFI Industry Fellowship for Multi-Gene Assay Cloud Computing Platform – (16/IFA/4342) and SAGE-CARE (Project ID: 644186).
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spelling Palu, Cintia C.Ribeiro-Alves, MarceloWu, YanxinLawlor, BrendanBaranov, Pavel V.Kelly, BrianWalsh, Paul2023-08-30T01:16:28Z2023-08-30T01:16:28Z2019PALU, Cintia C. et al. Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis. Frontiers in Genetics, v. 10, p. 1-10, May 2019.1664-8021https://www.arca.fiocruz.br/handle/icict/6025910.3389/fgene.2019.003561664-8021This work was supported by the grants from the Irish Research Council Enterprise Partnership; the SFI Industry Fellowship for Multi-Gene Assay Cloud Computing Platform – (16/IFA/4342) and SAGE-CARE (Project ID: 644186).School of Biochemistry and Cell Biology. University College Cork. Cork, Ireland / NSilico Life Science Ltd. Cork, Ireland.Oswaldo Cruz Foundation. Evandro Chagas National Institute of Infectious Diseases. Laboratory of Clinical Research on STD/AIDS. Rio de Janeiro, RJ, Brazil.NSilico Life Science Ltd. Cork, Ireland / Cork Institute of Technology. Cork, Ireland.NSilico Life Science Ltd. Cork, Ireland / Cork Institute of Technology. Cork, Ireland.School of Biochemistry and Cell Biology. University College Cork. Cork, Ireland / Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry. Moscow, Russia.NSilico Life Science Ltd. Cork, Ireland.NSilico Life Science Ltd. Cork, Ireland / Cork Institute of Technology. Cork, Ireland.One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to freely explore the data and test a new hypothesis with independence. Simplicity DiffExpress is a data-driven software platform dedicated to enabling non-bioinformaticians to take ownership of the differential expression analysis (DEA) step in a transcriptomics experiment while presenting the results in a comprehensible layout, which supports an efficient results exploration, information storage, and reproducibility. Simplicity DiffExpress' key component is the bespoke statistical model validation that guides the user through any necessary alteration in the dataset or model, tackling the challenges behind complex data analysis. The software utilizes edgeR, and it is implemented as part of the SimplicityTM platform, providing a dynamic interface, with well-organized results that are easy to navigate and are shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual DEA resources. Wet-lab collaborators can benefit from receiving their results in an organized interface. Simplicity DiffExpress is freely available for academic use, and it is cloud-based (https://simplicity.nsilico.com/dea).engFrontiers Research FoundationSimplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysisinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleRNA-seqData-drivenDifferential expression analysisDifferential gene expressionEdgeRStatistical modelingTranscriptomicsinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/60259/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALPalu_Cintia_etal_INI_2019.pdfPalu_Cintia_etal_INI_2019.pdfapplication/pdf6683840https://www.arca.fiocruz.br/bitstream/icict/60259/2/Palu_Cintia_etal_INI_2019.pdf098fee0d74cb0a5f204c135df0b5bc12MD52icict/602592023-08-29 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dc.title.en_US.fl_str_mv Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
title Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
spellingShingle Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
Palu, Cintia C.
RNA-seq
Data-driven
Differential expression analysis
Differential gene expression
EdgeR
Statistical modeling
Transcriptomics
title_short Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
title_full Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
title_fullStr Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
title_full_unstemmed Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
title_sort Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
author Palu, Cintia C.
author_facet Palu, Cintia C.
Ribeiro-Alves, Marcelo
Wu, Yanxin
Lawlor, Brendan
Baranov, Pavel V.
Kelly, Brian
Walsh, Paul
author_role author
author2 Ribeiro-Alves, Marcelo
Wu, Yanxin
Lawlor, Brendan
Baranov, Pavel V.
Kelly, Brian
Walsh, Paul
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Palu, Cintia C.
Ribeiro-Alves, Marcelo
Wu, Yanxin
Lawlor, Brendan
Baranov, Pavel V.
Kelly, Brian
Walsh, Paul
dc.subject.en.en_US.fl_str_mv RNA-seq
Data-driven
Differential expression analysis
Differential gene expression
EdgeR
Statistical modeling
Transcriptomics
topic RNA-seq
Data-driven
Differential expression analysis
Differential gene expression
EdgeR
Statistical modeling
Transcriptomics
description This work was supported by the grants from the Irish Research Council Enterprise Partnership; the SFI Industry Fellowship for Multi-Gene Assay Cloud Computing Platform – (16/IFA/4342) and SAGE-CARE (Project ID: 644186).
publishDate 2019
dc.date.issued.fl_str_mv 2019
dc.date.accessioned.fl_str_mv 2023-08-30T01:16:28Z
dc.date.available.fl_str_mv 2023-08-30T01:16:28Z
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.citation.fl_str_mv PALU, Cintia C. et al. Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis. Frontiers in Genetics, v. 10, p. 1-10, May 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/60259
dc.identifier.issn.none.fl_str_mv 1664-8021
dc.identifier.doi.none.fl_str_mv 10.3389/fgene.2019.00356
dc.identifier.eissn.none.fl_str_mv 1664-8021
identifier_str_mv PALU, Cintia C. et al. Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis. Frontiers in Genetics, v. 10, p. 1-10, May 2019.
1664-8021
10.3389/fgene.2019.00356
url https://www.arca.fiocruz.br/handle/icict/60259
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Research Foundation
publisher.none.fl_str_mv Frontiers Research Foundation
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/60259/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/60259/2/Palu_Cintia_etal_INI_2019.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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