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>

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

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
Depends On Me
Imports Me
Suggests Me
Links To Me
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/
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