@article{1bb631e761ed48fda6909bef9395e341,
title = "NACHO: an R package for quality control of NanoString nCounter data",
abstract = "Summary: The NanoString TM nCounter {\textregistered} 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 {\textregistered} data. ",
author = "Micka{\"e}l Canouil and Bouland, {Gerard A} and Am{\'e}lie Bonnefond and Philippe Froguel and {'t Hart}, {Leen M} and Slieker, {Roderick C}",
note = "Funding Information: This study was supported by grants from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 115881 (RHAPSODY). This Joint Undertaking receives support from the European Union{\textquoteright}s Horizon 2020 research and innovation programme and EFPIA. This work is supported by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 16.0097-2. The opinions expressed and arguments employed herein do not necessarily reflect the official views of these funding bodies. This study was supported by grants for funding of scientific research conducted in France and within the European Union: Centre National de la Recherche Scientifique, Universit{\'e} de Lille, Institut Pasteur de Lille, Contrat de Plan Etat-R{\'e}gion, Agence Nationale de la Recherche, {\textquoteleft}F{\'e}d{\'e}ration de Recherche{\textquoteright} 3508 Labex EGID (European Genomics Institute for Diabetes; ANR-10-LABX-46), ANR EQUIPEX LIGAN-MP (ANR-10-EQPX-07-01), European Research Council GEPIDIAB-294785. Publisher Copyright: {\textcopyright} 2019 The Author(s) 2019. Published by Oxford University Press. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2020",
month = feb,
day = "1",
doi = "10.1093/bioinformatics/btz647",
language = "English",
volume = "36",
pages = "970--971",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "3",
}