nCounter®Advanced Analysis Software

Version 2.0 now available! 

nCounter Advanced Analysis is a free, wizard-based add-on to nSolver™ Analysis Software for deeper data insights based on robust R statistics. Examine experimental trends, identify pathway-specific responses, and profile cell populations in sharable HTML reports.

  • Support for all DNA, RNA and protein CodeSets, including custom reagents and panels
  • Quick Analysis option for one-click data QC, normalization, and differential expression testing
  • Automatic incorporation of biological annotations and logical defaults for each panel
  • Save settings option to quickly re-run or modify any analysis
  • Shareable HTML reports for viewing in major web browsers

  1. Click on any of the below links to Log in or register for a NanoString account. Once you are logged in, the download will automatically start:
  2. (Optional) Download nCounter® Advanced Analysis Software (version 2.0.134)

Data QC and normalization
Get a high-level view of study design. See heatmaps, check for confounding variables, and evaluate the chosen normalization conditions.

Differential expression
Monitor how experimental factors influence expression changes at the target and pathway levels.

Cell profiling
Observe how the ratios of known immune cell type markers change based on treatments, time, or other variables.

Pathway scoring
Identify patterns of variation via pathway-by-pathway clustering.

RNA:Protein expression correlation
Compare the mRNA and protein levels from individual targets to uncover new relationships between transcriptional and translational responses.


SNV call summary
Summarize SNV variant events detected across samples


Fusion detection summary
Summarizes the fusion calls made in each gene across samples



Supported OS versions

Windows 8.1, Windows 10, Mac OS X 10.10 - 10.11


Pentium Core 2 Duo or Athlon X2 at 2.4 GHz


300 MB hard disk space + at least 1GB for caches.


1 GB required, 2 GB RAM recommended

Additional Java requirements for Macintosh

Java 7 or higher

Screen resolution


Graphics device

XQuartz for Macintosh users

Supported browsers

Edge, Chrome, Firefox, IE, Safari

R (required for Advanced Analysis only)

R 3.3.2

Additional requirements for Advanced Analysis only

Additional 3rd party packages, Internet connection with access to certain domains with static and dynamic IP address required for Advanced Analysis.

The probe annotation file contains the functional annotation and cell profiling associations for the genes in the panel.  This .csv file can be updated or modified by the user to accommodate custom analysis or the inclusion of annotations for Panel Plus genes in the advanced analysis report.  Where associations exist for a single gene, they are delimited by semicolons in the probe annotation field.  The user may need to upload a probe annotation file in the instance that the annotations are not built into the advanced analysis software or when the user desires to customize the analysis with a modified probe annotation file.

The option to load probe annotations when running an advanced analysis report is available under the custom analysis option:


The probe annotations, in .csv file format, is loaded through the import option.  The download option is available to view the current probe annotation, if loaded:


Once a probe annotation file is loaded, the status is indicated in the advanced analysis menu below the custom analysis option:



Annotation Files for Download:

CAR-T Panel Annotation File

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For Research Use Only. Not for use in diagnostic procedures.