nCounter®Advanced Analysis Software

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 immune cell populations in sharable HTML reports.

  • Support for all mRNA 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:
    1. (Optional) Download nCounter® Advanced Analysis Software

    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.

    Immune 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.



    Supported OS versions

    Windows 8.1, Windows 10, Mac OS X 10.10, OS X 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 25.10586, Chrome 51.0.2704, Firefox 43.0.1, IE 11.0.9600.18231, Safari 9.1.1

    R (required for Advanced Analysis only)

    R 3.1.1

    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.

    Click here to view publications

    Advanced Analysis Training

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