nCounter Academy: Data Analysis


Welcome to Data Analysis training for the nCounter® Platform!

Congratulations, you have successfully completed a run on either the nCounter MAX/FLEX or SPRINT instrument! The information in this section is dedicated towards providing a deeper insight into your experimental data and contains all the tools needed to analyze data collected from the nCounter for research use only. These resources represent a self-guided training curriculum that will enable any researcher to successfully analyze their NanoString data.

Below you will find resources for data analysis on nSolver™, the desktop-based software developed by NanoString, or on ROSALIND, a cloud-based data analysis option. Both data analysis options are offered free of charge to NanoString customers. A comparison between the software offerings can be found here.

All data analysis resources and description listed in this document are intended FOR RESEARCH USE ONLY. Not for diagnostics procedure.

Start Here with nSolver
Using nSolver Analysis Software
Additional Options
Need Help?
Start Here with nSolver

nSolver Download and Installation

Getting set up with nSolver basic suite and the advanced analysis module on your computer is easy! To get started, just follow these instructions:

  1. Download the basic nSolver suite. For instructions on how to install nSolver, please consult the nSolver user manual. Windows (64– or 32-bit) or for Mac
  2. Download the advanced analysis module. For instructions on installing the advanced analysis module, please consult the advanced analysis module user manual.
  3. Download R3.3.2. The advanced analysis module is compatible only with R3.3.2. If you have another version already installed on your computer, you will also have to install this version as well. Often this is done automatically during installation of the nSolver basic suite so you may not have to manually install R on your computer.
  4. (Mac only) Download and install XQuartz.
Using nSolver Analysis Software

Gene Expression Panels

Please join our on-demand nSolver data analysis webinars with content on the basic suite of nSolver and with the advanced analysis module with a focus on gene expression analysis. For new users, we will cover how to import your nCounter® data, perform quality control, normalize, and generate data plots. For advanced users, we teach you to build a custom Advanced Analysis and review the module outputs generated with your dataset.

Learn the basics of nSolver Advanced Analyses with nSolver


Follow along with the training webinars using the demo IO360 data set!

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Gene expression QC webinar
For information on analyzing data quality control metrics, please watch this webinar to get a thorough review of the QC metrics contained in each nCounter assay.

miRNA Panels

For miRNA data analysis with nSolver, please view this webinar discussing the fundamentals of analyzing a miRNA data set generated on the nCounter.

Additional Resources

For additional resources on nCounter data analysis applications please visit the nSolver support webpage, our webinar support page, or our FAQs on data analysis.


Data Analysis with ROSALIND

NanoString has partnered with ROSALIND to integrate our knowledge and expertise into an optimized analysis experience for the nCounter Platform. ROSALIND is cloud-based, runs in a web browser, and provides an intuitive experience that is designed with life scientists in mind. Please visit the website to sign up for a free account to analyze your nCounter data. Below is a 1-hour overview of the ROSALIND software for nCounter data analysis and a brief overview of setting up an analysis.

Watch On-Demand Here


ROSALIND also offers on demand training sessions covering the basics of analyzing nCounter data. During these sessions, they can cover the ROSALIND functionality for Experimental Set Up, Data QC, and Interactive Analysis and address participant questions.

Save Your Seat Here


Also consult the training video page for video tutorials on using ROSALIND for nCounter data analysis.

Additional Options

Consultation and Data Analysis Services

NanoString is dedicated to helping you get the most out of your data. In addition to technical support with nSolver, NanoString also offers customizable data analysis services (DAS) for a fee. Our highly trained and experienced staff will partner with you in designing and executing a personalized comprehensive data analysis plan. Contact us for more information and pricing.

In addition to completely custom data analysis options, the DAS also provides comprehensive reports for data generated by the IO360 and BC360 panels. An example output report for the BC360 panel is discussed in this webinar overview. Example data analysis reports for the IO360 and BC360 panels can be downloaded from the links below.

IO360 Demo DAS report
IO360 Time Course Demo DAS report
BC360 Demo DAS report
BC360 Time Series DAS Report
BC360 TNBC Demo DAS report

Visit the DAS website for more information on available data analysis services.

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