CNVfilteR

DOI: 10.18129/B9.bioc.CNVfilteR    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CNVfilteR.

Identifies false positives of CNV calling tools by using SNV calls

Bioconductor version: 3.10

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 <jmoreno at igtp.cat> and Bernat Gel <bgel at igtp.cat>

Maintainer: Jose Marcos Moreno-Cabrera <jmoreno at igtp.cat>

Installation

To install this package, start R (version "3.6") and enter:

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

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")

 

HTML	R Script	CNVfilteR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DNASeq, DataImport, Sequencing, Software, Visualization
Version	1.0.4
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
License	Artistic-2.0
Depends	R (>= 3.6)
Imports	IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods
LinkingTo
Suggests	knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked
SystemRequirements
Enhances
URL	https://github.com/jpuntomarcos/CNVfilteR
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	CNVfilteR_1.0.4.tar.gz
Windows Binary	CNVfilteR_1.0.4.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CNVfilteR_1.0.4.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