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NEUMA | Quantification of transcriptome from RNA-Seq data by effective length normalization

Evaluates mRNA abundances from RNA-Seq data. NEUMA is an algorithm dealing with the gene length effectively, suited for handling single-end and paired-end sequences. The method uses disjoint areas and reads to quantify gene transcript levels as well as isoform-specific expression levels. It was tested on real paired-end RNA-Seq data for two gastric cancer cell lines and by using computationally generated datasets.

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NEUMA classification

NEUMA specifications

Unique identifier:
Software type:
Restrictions to use:
Programming languages:
Normalization by Expected Uniquely Mappable Area
Command line interface
Operating system:
Computer skills:

NEUMA distribution


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NEUMA support


  • Sanghyuk Lee <>


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Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Biological Sciences, South Korea Advanced Institute of Science and Technology, Daejeon, South Korea; Ewha Research Center for Systems Biology (ERCSB), Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea

Funding source(s)

Supported by Korea Research Institute of Bioscience and Biotechnology Research Initiative Program [to S.L.]; ‘Systems Biology Infrastructure Establishment Grant’ provided by Gwangju Institute of Science & Technology; and Korea Healthcare Technology R&D Project [A084417].

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