CLOSE specifications

Information


Unique identifier OMICS_10892
Name Cna and LOh analysis with SEquencing data
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data CLOSE accepts BAM files, VCF files or initial segmentation files as input.
Output data CLOSE estimates segments copy number status.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Requirements DPpackage, grid, ggplot, VariantAnnotation
Maintained Yes

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Documentation


CLOSE article

CLOSE institution(s)
Department of Family, Population & Preventive Medicine, Stony Brook University, Stony Brook, NY, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA; Departments of Biostatistics and Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biostatistics, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Statistics, University of California, Davis, CA, USA; Department of Statistics, The Wharton School, University of Pennsylvania, PA, USA; Department of Pathology, Stony Brook University, Stony Brook, NY, USA
CLOSE funding source(s)
The National Cancer Institute (Yale SPORE in skin cancer, P50 CA121974); the National Institutes of Health (NIH) grants R01 CA082659 and P01CA142538; The NIH grant P20 CA192994

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