Introduction | Installation | Quick Start | Loading Copy-Number Data | Loading Variants Data | VCF free of artifacts | Minimun total depth | Regions to exclude | INDELs excluded by default | Other settings | Limitations | Identifying false positives | Scoring model for duplication CNVs | The margin.pct parameter | Plotting results | Session Info
Package: CNVfilteR 1.27.0
Jose Marcos Moreno-Cabrera
CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls
CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.
Authors:
CNVfilteR_1.27.0.tar.gz
CNVfilteR_1.27.0.zip(r-4.7)CNVfilteR_1.27.0.zip(r-4.6)CNVfilteR_1.27.0.zip(r-4.5)
CNVfilteR_1.27.0.tgz(r-4.6-any)CNVfilteR_1.27.0.tgz(r-4.5-any)
CNVfilteR_1.27.0.tar.gz(r-4.7-any)CNVfilteR_1.27.0.tar.gz(r-4.6-any)
CNVfilteR_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNVfilteR/json (API)
| # Install 'CNVfilteR' in R: |
| install.packages('CNVfilteR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jpuntomarcos/cnvfilter/issues
On BioConductor:CNVfilteR-1.27.0(bioc 3.24)CNVfilteR-1.26.0(bioc 3.23)
copynumbervariationsequencingdnaseqvisualizationdataimport
Last updated from:e829c8310c. Checks:6 NOTE, 2 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 296 | ||
| linux-devel-x86_64 | ERROR | 535 | ||
| source / vignettes | OK | 415 | ||
| linux-release-x86_64 | NOTE | 580 | ||
| macos-release-arm64 | NOTE | 406 | ||
| macos-oldrel-arm64 | NOTE | 249 | ||
| windows-devel | ERROR | 483 | ||
| windows-release | NOTE | 408 | ||
| windows-oldrel | NOTE | 405 | ||
| wasm-release | OK | 254 |
Exports:filterCNVsloadCNVcallsloadSNPsFromVCFloadVCFsplotAllCNVsplotScoringModelplotVariantsForCNV
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbamsignalsbase64encbezierBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercn.mopscodetoolscolorspaceCopyNumberPlotscpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdir.expiryensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigpngpracmaProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| auxAddCNcolumn | auxAddCNcolumn |
| auxGetVcfSource | auxGetVcfSource |
| auxProcessVariants | auxProcessVariants |
| filterCNVs | filterCNVs |
| getVariantScore | getVariantScore |
| loadCNVcalls | loadCNVcalls |
| loadSNPsFromVCF | loadSNPsFromVCF |
| loadVCFs | loadVCFs |
| plotAllCNVs | plotAllCNVs |
| plotVariantsForCNV | plotScoringModel |
| plotVariantsForCNV | plotVariantsForCNV |
