NACHO: an R package for quality control of NanoString nCounter data

Mickaël Canouil, Gerard A Bouland, Amélie Bonnefond, Philippe Froguel, Leen M 't Hart, Roderick C Slieker

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

Abstract

Summary: The NanoString TM 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.

Original languageEnglish
Pages (from-to)970-971
Number of pages2
JournalBioinformatics
Volume36
Issue number3
DOIs
Publication statusPublished - 1 Feb 2020

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