Package: rCNV 1.3.9000

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_1.3.9000.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'))

Peer review:

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

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:

cnv-analysiscopy-number-variationgene-duplicationgeneticsgenomicslandscape-geneticssnps

4.26 score 6 stars 4 scripts 329 downloads 24 exports 89 dependencies

Last updated 2 months agofrom:9e87b42428. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64NOTENov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64NOTENov 19 2024
R-4.4-mac-x86_64NOTENov 19 2024
R-4.4-mac-aarch64NOTENov 19 2024
R-4.3-win-x86_64NOTENov 19 2024
R-4.3-mac-x86_64NOTENov 19 2024
R-4.3-mac-aarch64NOTENov 19 2024

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

Dependencies:abindbackportsbase64encbslibcachemcheckmatecliclustercolorspacecorpcorcpp11data.tabledigestevaluatefansifarverfastmapfdrtoolfontawesomeforeignFormulafsggplot2glassoglueGPArotationgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobandjpegjquerylibjsonliteknitrlabelinglatticelavaanlifecyclemagrittrMASSMatrixmemoisemgcvmimemnormtmunsellnlmennetnumDerivpbapplypbivnormpillarpkgconfigplyrpngpsychqgraphquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml