CNVfilteR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

Identifies false positives of CNV calling tools by using SNV calls

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-8570-0345 , Bernat Gel [aut]

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

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

Jose Marcos Moreno-Cabrera, Bernat Gel. CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls. doi:10.18129/B9.bioc.CNVfilteR, R package version 1.27.0, https://bioconductor.org/packages/CNVfilteR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("CNVfilteR")

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

Documentation

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

browseVignettes("CNVfilteR")

CNVfilteR vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization
Version	1.27.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 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

Suggests	knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	CNVfilteR_1.27.0.tar.gz
Windows Binary (x86_64)	CNVfilteR_1.27.0.zip
macOS Binary (big-sur-x86_64)	CNVfilteR_1.27.0.tgz
macOS Binary (sonoma-arm64)	CNVfilteR_1.27.0.tgz
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