PennCNV specifications

Information

Unique identifier	OMICS_00729
Name	PennCNV
Software type	Application/Script
Interface	Command line interface
Restrictions to use	None
Biological technology	Illumina, Affymetrix
Operating system	Unix/Linux
Programming languages	C, Perl
Computer skills	Advanced
Stability	Stable
Maintained	Yes

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Documentation

Issues: https://github.com/WGLab/PennCNV/issues

Maintainer

Kai Wang <>

Additional information

http://penncnv.openbioinformatics.org/en/latest/

Publications for PennCNV

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

2008 Nucleic Acids Res

PMCID: 2577347

PMID: 18784189

DOI: 10.1093/nar/gkn556

Modeling genetic inheritance of copy number variations.

2008 Nucleic Acids Res

PMCID: 2588508

PMID: 18832372

DOI: 10.1093/nar/gkn641

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

2007 Genome Res

PMCID: 2045149

PMID: 17921354

DOI: 10.1101/gr.6861907

PennCNV IN pipeline

Evolution of Barrett’s esophagus through space and time at single-crypt and whole-biopsy levels

2018

PMCID: 5824808

PMID: 29476056

DOI: 10.1038/s41467-017-02621-x

[…] pass the quality control (0/1 column in supplementary data 1) and were excluded from further analysis. logr values were corrected for gc content bias using the genomic wave correction tool of the penncnv software suite41., the bioinformatics procedures and statistical tools to analyze the data are described in more detail in the supplementary methods (supplementary figs. 60–83, supplementary […]

PennCNV institution(s)

Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Center for Applied Genomics and Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA; Department of Mathematics, Georgetown University, Washington DC, USA

PennCNV funding source(s)

Supported by NARSAD Distinguished Investigator Award; University Research Foundation grant, McCabe Pilot Award from the University of Pennsylvania; National Institute of Health (grant R01HG004517), an Institute Development Award to the Center for Applied Genomics from the Children’s Hospital of Philadelphia.

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