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NanoStriDE: normalization and differential expression analysis of NanoString nCounter data

Christopher D Brumbaugh, Hyunsung J Kim, Mario Giovacchini and Nader Pourmand*

Author Affiliations

Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA

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BMC Bioinformatics 2011, 12:479  doi:10.1186/1471-2105-12-479

Published: 16 December 2011



The nCounter analysis system (NanoString Technologies, Seattle, WA) is a technology that enables the digital quantification of multiplexed target RNA molecules using color-coded molecular barcodes and single-molecule imaging. This system gives discrete counts of RNA transcripts and is capable of providing a high level of precision and sensitivity at less than one transcript copy per cell.


We have designed a web application compatible with any modern web browser that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis.


NanoStriDE allows biologists to take raw data produced by a NanoString nCounter analysis system and easily interpret differential expression analysis of this data represented through a heatmap. NanoStriDE is freely accessible to use on the NanoStriDE website and is available to use under the GPL v2 license.