SQuIRE specifications

Information


Unique identifier OMICS_29520
Name SQuIRE
Alternative name Software for Quantifying Interspersed Repeat Expression
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A transposable element.
Output data Some read counts and fragments per kilobase transcript per million reads (fpkm) for each TE locus.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version v0.9.9.9a
Stability Beta
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Kathleen Burns

Publication for Software for Quantifying Interspersed Repeat Expression

SQuIRE institution(s)
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
SQuIRE funding source(s)
Supported by National Institutes of Health (NIH) grants R01GM124531 and P50GM107632, and Department of Defense Congressionally Directed Medical Research Program (CDMRP) grant OC120390 and by a Teal Predoctoral Scholar award in association with OC120390.

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