Easy NanoString nCounter data analysis with the NanoTube

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

doi:10.1093/bioinformatics/btac762

Easy NanoString nCounter data analysis with the NanoTube

Bioinformatics. 2023 Jan 1;39(1):btac762. doi: 10.1093/bioinformatics/btac762.

Authors

Caleb A Class¹, Caiden J Lukan¹, Christopher A Bristow², Kim-Anh Do³

Affiliations

¹ Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA.
² TRACTION, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
³ Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Gene Library
Nanotubes*
Quality Control
Software*

Abstract

Publication types

MeSH terms

Grants and funding