NACHO: an R package for quality control of NanoString nCounter data.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 02 2020
01 02 2020
Historique:
received:
13
05
2019
revised:
24
07
2019
accepted:
14
08
2019
pubmed:
11
9
2019
medline:
18
9
2020
entrez:
11
9
2019
Statut:
ppublish
Résumé
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. NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31504159
pii: 5553566
doi: 10.1093/bioinformatics/btz647
pmc: PMC9883715
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
970-971Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Nucleic Acids Res. 2016 Nov 16;44(20):e151
pubmed: 27471031
Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
pubmed: 12184808
Bioinformatics. 2012 Jun 1;28(11):1546-8
pubmed: 22513995
Nucleic Acids Res. 2019 Jul 9;47(12):6073-6083
pubmed: 31114909
Genome Biol. 2009;10(6):R64
pubmed: 19531210
Oncotarget. 2015 Feb 28;6(6):4537-50
pubmed: 25738365