Package: CNVrd2 1.51.0

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_1.51.0.tar.gz
CNVrd2_1.51.0.zip(r-4.7)CNVrd2_1.51.0.zip(r-4.6)CNVrd2_1.51.0.zip(r-4.5)
CNVrd2_1.51.0.tgz(r-4.6-any)CNVrd2_1.51.0.tgz(r-4.5-any)
CNVrd2_1.51.0.tar.gz(r-4.7-any)CNVrd2_1.51.0.tar.gz(r-4.6-any)
CNVrd2_1.51.0.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.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:

ccl3l1data - Data of CCL3L1 gene
copynumberGroups - MXL population data
objectCNVrd2 - MXL population data
resultSegment - MXL population data

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

copynumbervariation snp sequencing software coverage linkagedisequilibrium clustering.jags cpp

4.92 score 3 stars 1 scripts 7 mentions 11 exports 83 dependencies

Last updated from:1e605d700f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	218
linux-devel-x86_64	NOTE	364
source / vignettes	OK	325
linux-release-x86_64	NOTE	351
macos-release-arm64	NOTE	183
macos-oldrel-arm64	NOTE	198
windows-devel	NOTE	236
windows-release	NOTE	217
windows-oldrel	NOTE	215
wasm-release	OK	165

Exports:calculateLDSNPandCNV countReadInWindow emnormalCNV groupBayesianCNVs groupCNVs identifyPolymorphicRegion plotCNVrd2 plotPolymorphicRegion searchGroupCNVs segmentSamples segmentSamplesUsingPopInformation

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli coda codetools cpp11 crayon curl DBI DelayedArray DNAcopy farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RColorBrewer RCurl restfulr Rhtslib rjags rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment sys VariantAnnotation vctrs viridisLite withr XML XVector yaml

A Markdown Vignette with knitr

Rendered fromCNVrd2.Rnwusingknitr::knitr

Last update: 2014-11-13
Started: 2013-10-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CNVrd2	CNVrd2-package
calculateLDSNPandCNV	calculateLDSNPandCNV
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 algorithm	emnormalCNV
Method 'emnormalCNV'	emnormalCNV-methods
MXL population data (The 1000 Genomes Project)	.Random.seed allGroups bamFiles copynumberGroups fcgr3bMXL objectCNVrd2 readCountMatrix resultSegment
groupBayesianCNVs	groupBayesianCNVs
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 groups	searchGroupCNVs
Method 'searchGroupCNVs'	searchGroupCNVs-methods
Implement the segmentation process	segmentSamples
Method 'segmentSamples'	segmentSamples,CNVrd2-method segmentSamples-methods
Implement the segmentation process for multiple populations	segmentSamplesUsingPopInformation
Method 'segmentSamplesUsingPopInformation'	segmentSamplesUsingPopInformation,CNVrd2-method segmentSamplesUsingPopInformation-methods
Class '"vectorORfactor"'	vectorORfactor-class