Simplicity DiffExpress: A bespoke cloud-based interface for RNA-seq differential expression modeling and analysis

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dc.contributor.authorPalu, Cintia C.
dc.contributor.authorRibeiro-Alves, Marcelo
dc.contributor.authorWu, Yanxin
dc.contributor.authorLawlor, Brendan
dc.contributor.authorBaranov, Pavel V.
dc.contributor.authorKelly, Brian
dc.contributor.authorWalsh, Paul
dc.contributor.funderIrish Research Councilen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2019-11-19T11:59:40Z
dc.date.available2019-11-19T11:59:40Z
dc.date.issued2019-05-14
dc.description.abstractOne 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 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, easy to navigate and shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual differential expression analysis 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).en
dc.description.sponsorship16/IFA/4342en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid356en
dc.identifier.citationPalu, C.C., Ribeiro-Alves, M., Wu, Y., Lawlor, B., Baranov, P.V., Kelly, B. and Walsh, P., 2019. Simplicity DiffExpress: a bespoke cloud-based interface for RNA-seq differential expression modeling and analysis. Frontiers in genetics, 10, (356). DOI:10.3389/fgene.2019.00356en
dc.identifier.doi10.3389/fgene.2019.00356en
dc.identifier.eissn1664-8021
dc.identifier.endpage12en
dc.identifier.journaltitleFrontiers in Geneticsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/9068
dc.identifier.volume10en
dc.language.isoenen
dc.publisherFrontiers Mediaen
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-RISE/644186/EU/SemAntically integrating Genomics with Electronic health records for Cancer CARE/SAGE-CAREen
dc.relation.urihttps://www.frontiersin.org/articles/10.3389/fgene.2019.00356
dc.rights© 2019 Palu, Ribeiro-Alves, Wu, Lawlor, Baranov, Kelly and Walshen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectDifferential expression analysisen
dc.subjectDifferential gene expressionen
dc.subjectStatistical modelingen
dc.subjectEdgeRen
dc.subjectTranscriptomicsen
dc.subjectRNA-seqen
dc.subjectData-drivenen
dc.titleSimplicity DiffExpress: A bespoke cloud-based interface for RNA-seq differential expression modeling and analysisen
dc.typeArticle (peer-reviewed)en
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