A Shiny application to enable intuitive resolution of Crambled: conflicting cellularity estimates [version 1; referees: awaiting peer review]

It 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. This article is included in the channel. RPackage Andy Lynch ( ) Corresponding author: [email protected] Lynch A. How to cite this article: A Shiny application to enable intuitive resolution of conflicting cellularity estimates Crambled: 2015, :1407 (doi: ) [version 1; referees: awaiting peer review] F1000Research 4 10.12688/f1000research.7453.1 © 2015 Lynch A. This is an open access article distributed under the terms of the , which Copyright: Creative Commons Attribution Licence permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AGL is supported by a Cancer Research UK programme grant (C14303/A20406) to Simon Tavaré and additionally Grant information: acknowledges funding from the European Commission through the Horizon 2020 project SOUND (Grant Agreement no. 633974). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: No competing interests were disclosed. 07 Dec 2015, :1407 (doi: ) First published: 4 10.12688/f1000research.7453.1 Referee Status: AWAITING PEER REVIEW 07 Dec 2015, :1407 (doi: ) First published: 4 10.12688/f1000research.7453.1 07 Dec 2015, :1407 (doi: ) Latest published: 4 10.12688/f1000research.7453.1 v1 Page 1 of 9 F1000Research 2015, 4:1407 Last updated: 09 DEC 2015