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Easy NanoString nCounter data analysis with the NanoTube.

Caleb A Class1, Caiden J Lukan1, Christopher A Bristow2

  • 1Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA.

Bioinformatics (Oxford, England)
|November 28, 2022
PubMed
Summary

NanoTube is an open-source pipeline for NanoString nCounter gene expression data analysis. This R package and web application simplify data processing, quality control, and analysis for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • NanoString nCounter technology provides a powerful method for gene expression profiling.
  • Analyzing NanoString data often requires specialized bioinformatics expertise and tools.
  • Existing pipelines may lack flexibility or user-friendliness for diverse research needs.

Purpose of the Study:

  • To introduce NanoTube, an open-source pipeline for streamlined NanoString nCounter gene expression data analysis.
  • To provide researchers with an accessible tool for data processing, quality control, normalization, and analysis.
  • To offer both a robust R package for bioinformaticians and a user-friendly web application for non-programmers.

Main Methods:

  • Development of an extensible R library implementing various gene expression analysis techniques.
  • Integration of advanced NanoString analysis functions within the R package.
  • Creation of an R-Shiny web application for simplified data analysis and visualization.

Main Results:

  • NanoTube effectively simplifies the entire workflow for NanoString nCounter gene expression data.
  • The R package offers comprehensive analytical capabilities and extensibility.
  • The web application provides an intuitive interface for researchers without programming experience.

Conclusions:

  • NanoTube enhances the accessibility and efficiency of NanoString data analysis.
  • The tool supports a wide range of users, from bioinformaticians to bench researchers.
  • This pipeline facilitates deeper insights from NanoString gene expression studies.