Easy NanoString nCounter data analysis with the NanoTube

Authors

Caleb A Class
Caiden J Lukan
Christopher A Bristow
Kim-Anh Do

Publication Date

1-1-2023

Journal

Bioinformatics

Abstract

Summary: The NanoTube is an open-source pipeline that simplifies the processing, quality control, normalization and analysis of NanoString nCounter gene expression data. It is implemented in an extensible R library, which performs a variety of gene expression analysis techniques and contains additional functions for integration with other R libraries performing advanced NanoString analysis techniques. Additionally, the NanoTube web application is available as a simple tool for researchers without programming expertise.

Availability and implementation: The NanoTube R package is available on Bioconductor under the GPL-3 license (https://www.bioconductor.org/packages/NanoTube/). The R-Shiny application can be downloaded at https://github.com/calebclass/Shiny-NanoTube, or a simplified version of this application can be run on all major browsers, at https://research.butler.edu/nanotube/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Keywords

Software, Gene Expression Profiling, Gene Library, Quality Control, Nanotubes

DOI

10.1093/bioinformatics/btac762

PMID

36440915

PMCID

PMC9805552

PubMedCentral® Posted Date

11-28-2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes