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dc.contributor.authorLynch, Andy
dc.date.accessioned2018-10-17T08:30:07Z
dc.date.available2018-10-17T08:30:07Z
dc.date.issued2015-12-07
dc.identifier.citationLynch , A 2015 , ' Crambled : a Shiny application to enable intuitive resolution of conflicting cellularity estimates ' , F1000Research , vol. 4 , 1407 . https://doi.org/10.12688/f1000research.7453.1en
dc.identifier.issn2046-1402
dc.identifier.otherPURE: 250727639
dc.identifier.otherPURE UUID: 8fba5c45-c46f-4bf7-94e7-81324db5c33f
dc.identifier.otherScopus: 84964484501
dc.identifier.otherORCID: /0000-0002-7876-7338/work/35946880
dc.identifier.urihttp://hdl.handle.net/10023/16248
dc.description.abstractIt is now commonplace to investigate tumour samples using whole-genome sequencing, and some commonly performed tasks are the estimation of cellularity (or sample purity), the genome-wide profiling of copy numbers, and the assessment of sub-clonal behaviours. Several tools are available to undertake these tasks, but often give conflicting results - not least because there is often genuine uncertainty due to a lack of model identifiability. Presented here is a tool, "Crambled", that allows for an intuitive visual comparison of the conflicting solutions. Crambled is implemented as a Shiny application within R, and is accompanied by example images from two use cases (one tumour sample with matched normal sequencing, and one standalone cell line example) as well as functions to generate the necessary images from any sequencing data set. Through the use of Crambled, a user may gain insight into why each tool has offered its given solution and combined with a knowledge of the disease being studied can choose between the competing solutions in an informed manner.
dc.format.extent13
dc.language.isoeng
dc.relation.ispartofF1000Researchen
dc.rightsCopyright © 2015 Lynch AG. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectCanceren
dc.subjectWhole-genome sequencingen
dc.subjectCellularityen
dc.subjectCopy numberen
dc.subjectSub-clonalityen
dc.subjectCell linesen
dc.subjectShinyen
dc.subjectRen
dc.subjectBioconductoren
dc.subjectQA76 Computer softwareen
dc.subjectRC0254 Neoplasms. Tumors. Oncology (including Cancer)en
dc.subjectBiochemistry, Genetics and Molecular Biology(all)en
dc.subjectImmunology and Microbiology(all)en
dc.subjectMedicine(all)en
dc.subjectPharmacology, Toxicology and Pharmaceutics(all)en
dc.subjectDASen
dc.subject.lccQA76en
dc.subject.lccRC0254en
dc.titleCrambled : a Shiny application to enable intuitive resolution of conflicting cellularity estimatesen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.Statisticsen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.identifier.doihttps://doi.org/10.12688/f1000research.7453.1
dc.description.statusPeer revieweden


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