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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 forum

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NEUMA classification

NEUMA specifications

Unique identifier:
OMICS_01281
Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Perl
Version:
1.1.0
Maintained:
Yes
Name:
Normalization by Expected Uniquely Mappable Area
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable

NEUMA distribution

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NEUMA support

Maintainer

  • Sanghyuk Lee <>

Credits

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Publications

Institution(s)

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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