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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>

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

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

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

Details

biocViews CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization
Version 1.17.0
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
See More
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_1.17.0.tar.gz
Windows Binary CNVfilteR_1.17.0.zip (64-bit only)
macOS Binary (x86_64) CNVfilteR_1.17.0.tgz
macOS Binary (arm64) CNVfilteR_1.17.0.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/
Package Downloads Report Download Stats