CNVfilteR

Identifies false positives of CNV calling tools by using SNV calls

Bioconductor version: 3.23 · Package version: 1.26.0

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

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CNVfilteR")

Details

Maintainer	Jose Marcos Moreno-Cabrera <jpuntomarcos@gmail.com>
Author	Jose Marcos Moreno-Cabrera [aut, cre] (ORCID: <https://orcid.org/0000-0001-8570-0345>), Bernat Gel [aut]
License	Artistic-2.0
URL	https://github.com/jpuntomarcos/CNVfilteR
Bug Reports	https://github.com/jpuntomarcos/CNVfilteR/issues
Downloads rank	295
Source branch	RELEASE_3_23
biocViews	CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization

Documentation

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

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Source package

Dependencies

Depends: R (>= 4.3)

Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods

Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown