Package: CNVfilteR 1.26.0

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:Jose Marcos Moreno-Cabrera [aut, cre], Bernat Gel [aut]

CNVfilteR_1.26.0.tar.gz
CNVfilteR_1.26.0.zip(r-4.7)CNVfilteR_1.26.0.zip(r-4.6)CNVfilteR_1.26.0.zip(r-4.5)
CNVfilteR_1.26.0.tgz(r-4.6-any)CNVfilteR_1.26.0.tgz(r-4.5-any)
CNVfilteR_1.26.0.tar.gz(r-4.7-any)CNVfilteR_1.26.0.tar.gz(r-4.6-any)
CNVfilteR_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CNVfilteR/json (API)
NEWS

# Install 'CNVfilteR' in R:

install.packages('CNVfilteR', repos = c('https://bioc-release.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)

copynumbervariation sequencing dnaseq visualization dataimport

5.26 score 6 stars 2 scripts 296 downloads 7 exports 133 dependencies

Last updated from:65126b117b (on RELEASE_3_23). Checks:6 NOTE, 2 ERROR, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	296
linux-devel-x86_64	ERROR	429
source / vignettes	OK	389
linux-release-x86_64	NOTE	521
macos-release-arm64	NOTE	359
macos-oldrel-arm64	NOTE	287
windows-devel	ERROR	409
windows-release	NOTE	439
windows-oldrel	NOTE	430
wasm-release	OK	262

Exports:filterCNVs loadCNVcalls loadSNPsFromVCF loadVCFs plotAllCNVs plotScoringModel plotVariantsForCNV

Dependencies:abind AnnotationDbi AnnotationFilter askpass assertthat backports bamsignals base64enc bezier BH Biobase BiocGenerics BiocIO biocmake BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster cn.mops codetools colorspace CopyNumberPlots cpp11 crayon curl data.table DBI DelayedArray dichromat digest dir.expiry ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite karyoploteR KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime nnet openssl pkgconfig png pracma ProtGenerics R6 rappdirs RColorBrewer Rcpp RCurl regioneR restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tinytex UCSC.utils VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml

CNVfilteR: Remove false positives of CNV calling tools by using SNV calls

Jose Marcos Moreno-Cabrera [email protected] and Bernat Gel [email protected]

Rendered fromCNVfilteR.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2022-12-02
Started: 2019-10-01

Citation

Development and contributors

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