ArticleBioinformatics (Oxford, England)2020
NACHO: an R package for quality control of NanoString nCounter data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- Differential transcriptional and epigenetic signatures in CD4Journal of translational autoimmunity · 2026Article
- shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data.Bioinformatics (Oxford, England) · 2025Article
- Machine Learning-Based Ensemble Feature Selection and Nested Cross-Validation for miRNA Biomarker Discovery in Usher Syndrome.Bioengineering (Basel, Switzerland) · 2025Article
- Challenges and opportunities in processing NanoString nCounter data.Computational and structural biotechnology journal · 2024Review
- Genotype Characterization and MiRNA Expression Profiling in Usher Syndrome Cell Lines.International journal of molecular sciences · 2024Article
- GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization.Bioinformatics (Oxford, England) · 2024Article
- Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis.Research square · 2024Article
- nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis.Bioinformatics (Oxford, England) · 2024Article
- Transcriptomic profiles of multiple organ dysfunction syndrome phenotypes in pediatric critical influenza.Frontiers in immunology · 2023Article
- Easy NanoString nCounter data analysis with the NanoTube.Bioinformatics (Oxford, England) · 2023Article
- Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic.British journal of cancer · 2022Article
- Exploiting 4-1BB immune checkpoint to enhance the efficacy of oncolytic virotherapy for diffuse intrinsic pontine gliomas.JCI insight · 2022Article
- An approach for normalization and quality control for NanoString RNA expression data.Briefings in bioinformatics · 2021Article
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryThe 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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