Mickaël Canouil1, Gerard A Bouland2, Amélie Bonnefond1,3, Philippe Froguel1,3, Leen M 't Hart2,4,5, Roderick C Slieker2,4. 1. Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8199 - EGID, F-59000 Lille, France. 2. Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands. 3. Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London SW7 2AZ, UK. 4. Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, VU University Medical Center, Amsterdam 1081 HV, The Netherlands. 5. Molecular Epidemiology Section, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands.
Abstract
SUMMARY: The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO ('NAnostring quality Control dasHbOard'), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data. AVAILABILITY AND IMPLEMENTATION: NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO ('NAnostring quality Control dasHbOard'), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data. AVAILABILITY AND IMPLEMENTATION:NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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