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CQN | Removing technical variability in RNA-seq data

Allows users to study RNA-Seq data. CQN is an algorithm using generalized regression to remove systematic bias introduced by deterministic features such as guanine-cytosine (GC)-content and quantile normalization. This permits the correction of global distortions. It includes other functions permitting the inclusion of map ability or elaborate models of sequence effects.

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CQN classification

CQN specifications

Unique identifier:
Software type:
Restrictions to use:
Programming languages:
Computer skills:
Conditional Quantile Normalization
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Artistic License version 2.0

CQN distribution


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CQN support



  • Kasper Daniel Hansen <>
  • Zhijin Wu <>


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Department of Biostatistics, Brown University, Providence, RI, USA

Funding source(s)

Supported by the National Institutes of Health (R01HG004059) and National Science Foundation (DBI-1054905).

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