:: DESCRIPTION
CNVtools is an R package for performing robust case control and quantitative trait association analyses of Copy Number Variants.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A robust statistical method for case-control association testing with Copy Number Variation.
Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME.
Nature Genetics, 2008 Oct;40(10):1245-52
:: DESCRIPTION
PiCNV (Phasing and inheritance of Copy Number Variants) enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data.
::DEVELOPER
Department of Bioinformatics, University of Tartu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M
:: DESCRIPTION
Piet provides some segmentation tools, using fused lasso, group fused lasso and generalized fused lasso (GFL), for analysis of individual or multiple sequences of CNV data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Z. Zhang, K. Lange, C. Sabatti (2012)
Reconstructing DNA copy number by joint segmentation of multiple sequences
:: DESCRIPTION
CoNVEM (Copy Number Variation Expectation Maximisation) is an expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM)
::DEVELOPER
Tom Gaunt’s group in the MRC IEU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Hum Mutat. 2010 Apr;31(4):414-20. doi: 10.1002/humu.21199.
An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): insights into population allelic architecture and its mutational history.
Gaunt TR1, Rodriguez S, Guthrie PA, Day IN.
:: DESCRIPTION
MinimumDistance is an R package for detecting de novo copy number alterations from SNP arrays in case-parent trio designs
::DEVELOPER
Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2012 Dec 12;13:330. doi: 10.1186/1471-2105-13-330.
Fast detection of de novo copy number variants from SNP arrays for case-parent trios.
Scharpf RB1, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I.
:: DESCRIPTION
FSDA is an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome.
:: DEVELOPER
Computational Biology Lab at the University of Toronto
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.
Arbabi A, Rampášek L, Brudno M.
Bioinformatics. 2016 Apr 5. pii: btw178.
:: DESCRIPTION
PSE-HMM is a tool for the genome-wide CNV detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies an HMM with Position-Specific Emission probabilities for modeling different aberrations in the mate pairs, after being mapped to the reference genome.
::DEVELOPER
School of Biological Sciences, Iran
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2016 Nov 3;18(1):30. doi: 10.1186/s12859-016-1296-y.
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.
Malekpour SA, Pezeshk H, Sadeghi M
:: DESCRIPTION
CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.
:: DESCRIPTION
CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region
CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.
:: DESCRIPTION
CLAMMS (Copy number estimation using Lattice-Aligned Mixture Models) is an algorithm for calling copy number variants (CNVs) from exome sequencing read depths.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.
Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG.
Bioinformatics. 2015 Sep 17. pii: btv547.
