Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates
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Lynch, A. (2015). Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates. F1000research, 4 (1407)https://doi.org/10.12688/f1000research.7453.1
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.
AGL is supported by a Cancer Research UK programme grant (C14303/A20406) to Simon Tavaré and additionally acknowledges funding from the European Commission through the Horizon 2020 project SOUND (Grant Agreement no. 633974).
European Commission Horizon 2020 (H2020) Societal Challenges (633974)
External DOI: https://doi.org/10.12688/f1000research.7453.1
This record's URL: https://www.repository.cam.ac.uk/handle/1810/252854
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Licence URL: http://creativecommons.org/licenses/by/4.0/