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Identifies false positives of CNV calling tools by using SNV calls

Bioconductor version: Release (3.18)

CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.

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

Maintainer: Jose Marcos Moreno-Cabrera <jpuntomarcos at gmail.com>

Citation (from within R, enter citation("CNVfilteR")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CNVfilteR vignette HTML R Script
Reference Manual PDF


biocViews CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 4.3)
Imports IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods
System Requirements
URL https://github.com/jpuntomarcos/CNVfilteR
Bug Reports https://github.com/jpuntomarcos/CNVfilteR/issues
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Suggests knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CNVfilteR_1.16.0.tar.gz
Windows Binary CNVfilteR_1.16.0.zip
macOS Binary (x86_64) CNVfilteR_1.16.0.tgz
macOS Binary (arm64) CNVfilteR_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CNVfilteR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CNVfilteR
Bioc Package Browser https://code.bioconductor.org/browse/CNVfilteR/
Package Short Url https://bioconductor.org/packages/CNVfilteR/
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