IsoEM protocols

IsoEM specifications


Unique identifier OMICS_01278
Name IsoEM
Alternative names IsoEM2/IsoDE2, IsoEM/IsoDE
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A set of known isoforms and a file with aligned reads.
Input format SAM + GTF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0.0
Stability Stable
Source code URL
Maintained Yes



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  • person_outline iim03001 <>
  • person_outline Igor Mandric <>

Additional information

IsoEM2: IsoDE2:

Publications for IsoEM

IsoEM IN pipeline

PMCID: 3851429
PMID: 24268045
DOI: 10.1186/1471-2105-14-S14-S4

[…] integrated into a tool pipeline. however, following our tool and file independent design approach, other reconstruction tools such as isolasso[29] or trip[30], and/or other quantification tools isoem[31] or rsem[32] may be utilized. finally, multiple myeloma and its associated cancer biology knowledge is utilized and structured to further illustrate the disease-based cross reference […]

IsoEM institution(s)
Department of Computer Science, Georgia State University, Atlanta, GA, USA; Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA; Immunology Department, University of Connecticut Health Center, Farmington, CT, USA
IsoEM funding source(s)
Supported in part by a GSU Molecular Basis of Disease Fellowship and NSF awards 1564899, 1564936, 1618347, and 16119110.

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