CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

AuthorHoang Tan Nguyen, Tony R Merriman and Mik Black
Date of publicationNone
MaintainerHoang Tan Nguyen <hoangtannguyenvn@gmail.com>
LicenseGPL-2
Version1.12.0
https://github.com/hoangtn/CNVrd2

View on Bioconductor

Functions

allGroups Man page
bamFiles Man page
calculateLDSNPandCNV Man page
ccl3l1data Man page
clusteringCNVs-class Man page
CNVrd2-class Man page
CNVrd2-package Man page
copynumberGroups Man page
countReadInWindow Man page
countReadInWindow,CNVrd2-method Man page
countReadInWindow-methods Man page
emnormalCNV Man page
emnormalCNV,clusteringCNVs-method Man page
emnormalCNV-methods Man page
fcgr3bMXL Man page
groupBayesianCNVs Man page
groupCNVs Man page
groupCNVs,clusteringCNVs-method Man page
groupCNVs-methods Man page
identifyPolymorphicRegion Man page
identifyPolymorphicRegion,CNVrd2-method Man page
identifyPolymorphicRegion-methods Man page
numericOrNULL-class Man page
objectCluster Man page
objectCNVrd2 Man page
plotCNVrd2 Man page
plotCNVrd2,CNVrd2-method Man page
plotCNVrd2-methods Man page
plotPolymorphicRegion Man page
plotPolymorphicRegion,CNVrd2-method Man page
plotPolymorphicRegion-methods Man page
.Random.seed Man page
readCountMatrix Man page
resultSegment Man page
searchGroupCNVs Man page
searchGroupCNVs,clusteringCNVs-method Man page
searchGroupCNVs-methods Man page
segmentSamples Man page
segmentSamples,CNVrd2-method Man page
segmentSamples-methods Man page
segmentSamplesUsingPopInformation Man page
segmentSamplesUsingPopInformation,CNVrd2-method Man page
segmentSamplesUsingPopInformation-methods Man page
vectorORfactor-class Man page

Files

CNVrd2/DESCRIPTION
CNVrd2/NAMESPACE
CNVrd2/R
CNVrd2/R/AllClasses.R CNVrd2/R/AllGenerics.R CNVrd2/R/calculateLDSNPandCNV.R CNVrd2/R/countReadInWindow.R CNVrd2/R/emnormalCNV.R CNVrd2/R/groupBayesianCNVs.R CNVrd2/R/groupCNVs.R CNVrd2/R/identifyPolymorphicRegion.R CNVrd2/R/plotCNVrd2.R CNVrd2/R/plotPolymorphicRegion.R CNVrd2/R/searchGroupCNVs.R CNVrd2/R/segmentSamples.R CNVrd2/R/segmentSamplesUsingPopInformation.R
CNVrd2/build
CNVrd2/build/vignette.rds
CNVrd2/data
CNVrd2/data/ccl3l1data.txt.gz
CNVrd2/data/fcgr3bMXL.RData
CNVrd2/inst
CNVrd2/inst/doc
CNVrd2/inst/doc/CNVrd2.R
CNVrd2/inst/doc/CNVrd2.Rnw
CNVrd2/inst/doc/CNVrd2.pdf
CNVrd2/inst/extdata
CNVrd2/inst/extdata/ccl3l1data.txt
CNVrd2/inst/extdata/chr1.161600000.161611000.vcf.gz
CNVrd2/inst/extdata/chr1.161600000.161611000.vcf.gz.tbi
CNVrd2/inst/extdata/chr17.34800000.34830000.vcf.gz
CNVrd2/inst/extdata/chr17.34800000.34830000.vcf.gz.tbi
CNVrd2/inst/extdata/chr17.34815000.34823000.vcf.gz
CNVrd2/inst/extdata/chr17.34815000.34823000.vcf.gz.tbi
CNVrd2/man
CNVrd2/man/CNVrd2-class.Rd CNVrd2/man/CNVrd2-package.Rd CNVrd2/man/calculateLDSNPandCNV.Rd CNVrd2/man/ccl3l1data.Rd CNVrd2/man/clusteringCNVs-class.Rd CNVrd2/man/countReadInWindow-methods.Rd CNVrd2/man/countReadInWindow.Rd CNVrd2/man/emnormalCNV-methods.Rd CNVrd2/man/emnormalCNV.Rd CNVrd2/man/fcgr3bMXL.Rd CNVrd2/man/groupBayesianCNVs.Rd CNVrd2/man/groupCNVs-methods.Rd CNVrd2/man/groupCNVs.Rd CNVrd2/man/identifyPolymorphicRegion-methods.Rd CNVrd2/man/identifyPolymorphicRegion.Rd CNVrd2/man/numericOrNULL-class.Rd CNVrd2/man/plotCNVrd2-methods.Rd CNVrd2/man/plotCNVrd2.Rd CNVrd2/man/plotPolymorphicRegion-methods.Rd CNVrd2/man/plotPolymorphicRegion.Rd CNVrd2/man/searchGroupCNVs-methods.Rd CNVrd2/man/searchGroupCNVs.Rd CNVrd2/man/segmentSamples-methods.Rd CNVrd2/man/segmentSamples.Rd CNVrd2/man/segmentSamplesUsingPopInformation-methods.Rd CNVrd2/man/segmentSamplesUsingPopInformation.Rd CNVrd2/man/vectorORfactor-class.Rd
CNVrd2/vignettes
CNVrd2/vignettes/CNVrd2.Rnw
CNVrd2/vignettes/refCNVrd2.bib

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