lncScore specifications

Information


Unique identifier OMICS_13563
Name lncScore
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Transcripts sequences
Input format BED, FASTA
Output data Table with transcript identifier, coding scores
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements
Perl, SciKit-learn, pysam
Maintained Yes

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Documentation


Maintainer


  • person_outline Jian Zhao <>

Publication for lncScore

lncScore in publication

PMCID: 5751786
PMID: 29297275
DOI: 10.1186/s12859-017-1890-7

[…] billion rna-seq reads generated from 80 human and 66 rat brain tissue samples [, ] were processed and assembled utilizing our method. a coding-potential assessment of the assembled transcripts using lncscore [] yielded 33,203 human and 53,782 rat lncrna candidates. to reduce false positives that could be generated by assembly [] and coding-potential [, ] methods, we applied several critical […]


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lncScore institution(s)
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
lncScore funding source(s)
The study was supported by grants from National Natural Science Foundation of China (No. 61571223, No. 61171191), Specialized Research Fund for the Doctoral Program of Higher Education (No. 20133218110016), the “Six Talent Peak” Project of Jiangsu Province under Grant No. SWYY-021, and NIH grant HG006465.

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