Package: CNVrd2 1.50.0

Hoang Tan Nguyen

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.

Authors:Hoang Tan Nguyen, Tony R Merriman and Mik Black

CNVrd2_1.50.0.tar.gz
CNVrd2_1.50.0.zip(r-4.7-any)CNVrd2_1.50.0.zip(r-4.6-any)CNVrd2_1.50.0.zip(r-4.5-any)
CNVrd2_1.50.0.tgz(r-4.6-any)CNVrd2_1.50.0.tgz(r-4.5-any)
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CNVrd2_1.50.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CNVrd2/json (API)

# Install 'CNVrd2' in R:
install.packages('CNVrd2', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hoangtn/cnvrd2/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:CNVrd2-1.51.0(bioc 3.24)CNVrd2-1.50.0(bioc 3.23)

copynumbervariationsnpsequencingsoftwarecoveragelinkagedisequilibriumclustering.jagscpp

3.92 score 3 stars 5 scripts 624 downloads 7 mentions 11 exports 82 dependencies

Last updated from:29394d13e7 (on RELEASE_3_23). Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR186
linux-develWARNING345
source / vignettesERROR3220
linux-releaseWARNING303
macos-releaseWARNING166
macos-oldrelWARNING178
windows-develWARNING284
windows-releaseWARNING237
windows-oldrelWARNING214
wasm-releaseOK145

Exports:calculateLDSNPandCNVcountReadInWindowemnormalCNVgroupBayesianCNVsgroupCNVsidentifyPolymorphicRegionplotCNVrd2plotPolymorphicRegionsearchGroupCNVssegmentSamplessegmentSamplesUsingPopInformation

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodacodetoolscpp11crayoncurlDBIDelayedArrayDNAcopyfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RColorBrewerRCurlrestfulrRhtslibrjagsrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsysVariantAnnotationvctrsviridisLitewithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
CNVrd2CNVrd2-package
calculateLDSNPandCNVcalculateLDSNPandCNV
Data of CCL3L1 gene (The 1000 Genomes Project)ccl3l1data
Class '"clusteringCNVs"'clusteringCNVs-class emnormalCNV,clusteringCNVs-method groupCNVs,clusteringCNVs-method objectCluster searchGroupCNVs,clusteringCNVs-method
Class '"CNVrd2"'CNVrd2-class countReadInWindow,CNVrd2-method plotCNVrd2,CNVrd2-method
Obtain read counts in constant windows.countReadInWindow
Method 'countReadInWindow'countReadInWindow-methods
Implement the EM algorithmemnormalCNV
Method 'emnormalCNV'emnormalCNV-methods
MXL population data (The 1000 Genomes Project).Random.seed allGroups bamFiles copynumberGroups fcgr3bMXL objectCNVrd2 readCountMatrix resultSegment
groupBayesianCNVsgroupBayesianCNVs
Cluster segmentation scores into groups.groupCNVs
Method 'groupCNVs'groupCNVs-methods
Identity polymorphic regions.identifyPolymorphicRegion
Methods for Function 'identifyPolymorphicRegion'identifyPolymorphicRegion,CNVrd2-method identifyPolymorphicRegion-methods
Class '"numericOrNULL"'numericOrNULL-class
Plot traces of samples.plotCNVrd2
Method 'plotCNVrd2'plotCNVrd2-methods
Plot polymorphic regions.plotPolymorphicRegion
Methods for Function 'plotPolymorphicRegion'plotPolymorphicRegion,CNVrd2-method plotPolymorphicRegion-methods
Choose a number of CN groupssearchGroupCNVs
Method 'searchGroupCNVs'searchGroupCNVs-methods
Implement the segmentation processsegmentSamples
Method 'segmentSamples'segmentSamples,CNVrd2-method segmentSamples-methods
Implement the segmentation process for multiple populationssegmentSamplesUsingPopInformation
Method 'segmentSamplesUsingPopInformation'segmentSamplesUsingPopInformation,CNVrd2-method segmentSamplesUsingPopInformation-methods
Class '"vectorORfactor"'vectorORfactor-class