{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T18:49:32Z","timestamp":1757702972794,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T00:00:00Z","timestamp":1566518400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Innovative Medicines Initiative 2 Joint Undertaking","award":["115881"],"award-info":[{"award-number":["115881"]}]},{"name":"RHAPSODY"},{"name":"European Union: Centre National de la Recherche Scientifique"},{"name":"Universit\u00e9 de Lille, Institut Pasteur de Lille"},{"name":"European Genomics Institute for Diabetes","award":["ANR-10-LABX-46","ANR-10-EQPX-07-01"],"award-info":[{"award-number":["ANR-10-LABX-46","ANR-10-EQPX-07-01"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["GEPIDIAB-294785"],"award-info":[{"award-number":["GEPIDIAB-294785"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The NanoStringTM nCounter\u00ae 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 (\u2018NAnostring quality Control dasHbOard\u2019), 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\u00ae data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NACHO is available as an R-package on CRAN and the development version on GitHub https:\/\/github.com\/mcanouil\/NACHO.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz647","type":"journal-article","created":{"date-parts":[[2019,8,15]],"date-time":"2019-08-15T19:12:48Z","timestamp":1565896368000},"page":"970-971","source":"Crossref","is-referenced-by-count":23,"title":["<i>NACHO:<\/i> an R package for quality control of NanoString nCounter data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3396-4549","authenticated-orcid":false,"given":"Micka\u00ebl","family":"Canouil","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Lille, CNRS, Institut Pasteur de Lille , UMR 8199 - EGID, F-59000 Lille, France"}]},{"given":"Gerard A","family":"Bouland","sequence":"additional","affiliation":[{"name":"Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands"}]},{"given":"Am\u00e9lie","family":"Bonnefond","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lille, CNRS, Institut Pasteur de Lille , UMR 8199 - EGID, F-59000 Lille, France"},{"name":"Department of Medicine, Section of Genomics of Common Disease, Imperial College London , London SW7 2AZ, UK"}]},{"given":"Philippe","family":"Froguel","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lille, CNRS, Institut Pasteur de Lille , UMR 8199 - EGID, F-59000 Lille, France"},{"name":"Department of Medicine, Section of Genomics of Common Disease, Imperial College London , London SW7 2AZ, UK"}]},{"given":"Leen M","family":"\u2019t Hart","sequence":"additional","affiliation":[{"name":"Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands"},{"name":"Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, VU University Medical Center , Amsterdam 1081 HV, The Netherlands"},{"name":"Molecular Epidemiology Section, Department of Biomedical Data Sciences, Leiden University Medical Center , Leiden 2333 ZC, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0961-9152","authenticated-orcid":false,"given":"Roderick C","family":"Slieker","sequence":"additional","affiliation":[{"name":"Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands"},{"name":"Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, VU University Medical Center , Amsterdam 1081 HV, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2019,8,23]]},"reference":[{"key":"2023013110092889900_btz647-B1","doi-asserted-by":"crossref","first-page":"4537","DOI":"10.18632\/oncotarget.3005","article-title":"Identification of a microRNA signature associated with risk of distant metastasis in nasopharyngeal carcinoma","volume":"6","author":"Bruce","year":"2015","journal-title":"Oncotarget"},{"key":"2023013110092889900_btz647-B2","doi-asserted-by":"crossref","first-page":"R64","DOI":"10.1186\/gb-2009-10-6-r64","article-title":"A novel and universal method for microRNA RT-qPCR data normalization","volume":"10","author":"Mestdagh","year":"2009","journal-title":"Genome Biol"},{"key":"2023013110092889900_btz647-B3","doi-asserted-by":"crossref","first-page":"6073","DOI":"10.1093\/nar\/gkz433","article-title":"A new normalization for Nanostring nCounter 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