CNVfilteR

DOI: 10.18129/B9.bioc.CNVfilteR  

This is the development version of CNVfilteR; for the stable release version, see CNVfilteR.

Identifies false positives of CNV calling tools by using SNV calls

Bioconductor version: Development (3.19)

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>

Installation

To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CNVfilteR")

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

Documentation

PDF		Reference Manual

Details

biocViews	CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization
Version	1.17.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 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
LinkingTo
Suggests	knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/jpuntomarcos/CNVfilteR
BugReports	https://github.com/jpuntomarcos/CNVfilteR/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CNVfilteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVfilteR
Package Short Url	https://bioconductor.org/packages/CNVfilteR/
Package Downloads Report	Download Stats