Package: rCNV 1.3.900

rCNV: Detect Copy Number Variants from SNPs Data

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

Authors:Piyal Karunarathne [aut, cre], Qiujie Zhou [aut], Klaus Schliep [aut], Pascal Milesi [aut]

rCNV_1.3.900.tar.gz
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rCNV.pdf |rCNV.html✨
rCNV/json (API)
NEWS

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

Bug tracker:https://github.com/piyalkarum/rcnv/issues

Pkgdown site:https://piyalkarum.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ADnorm - Normalized allele depth example data
  • ADtable - Allele Depth (AD) example data
  • alleleINF - Allele info example data

On CRAN:

Conda:

cnv-analysiscopy-number-variationgene-duplicationgeneticsgenomicslandscape-geneticssnpscpp

4.26 score 6 stars 4 scripts 300 downloads 24 exports 89 dependencies

Last updated 23 days agofrom:f28bf8dc57. Checks:1 OK, 11 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 04 2025
R-4.5-win-x86_64NOTEMar 04 2025
R-4.5-mac-x86_64NOTEMar 04 2025
R-4.5-mac-aarch64NOTEMar 04 2025
R-4.5-linux-x86_64NOTEMar 04 2025
R-4.4-win-x86_64NOTEMar 04 2025
R-4.4-mac-x86_64NOTEMar 04 2025
R-4.4-mac-aarch64NOTEMar 04 2025
R-4.4-linux-x86_64NOTEMar 04 2025
R-4.3-win-x86_64NOTEMar 04 2025
R-4.3-mac-x86_64NOTEMar 04 2025
R-4.3-mac-aarch64NOTEMar 04 2025

Exports:ad.correctallele.freqallele.infocnvcpm.normaldepthVsSampledup.plotdup.validatedupGetexportVCFget.missgt.formath.zygosityhetTgenmafnorm.factpower.biasreadVCFrelatednesssig.hetssim.alsvcf.statvstvstPermutation

Dependencies:abindbackportsbase64encbslibcachemcheckmatecliclustercolorspacecorpcorcpp11data.tabledigestevaluatefansifarverfastmapfdrtoolfontawesomeforeignFormulafsggplot2glassoglueGPArotationgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobandjpegjquerylibjsonliteknitrlabelinglatticelavaanlifecyclemagrittrMASSMatrixmemoisemgcvmimemnormtmunsellnlmennetnumDerivpbapplypbivnormpillarpkgconfigplyrpngpsychqgraphquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml