CNVPanelizer

DOI: 10.18129/B9.bioc.CNVPanelizer    

Reliable CNV detection in targeted sequencing applications

Bioconductor version: Release (3.13)

A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.

Author: Cristiano Oliveira [aut], Thomas Wolf [aut, cre], Albrecht Stenzinger [ctb], Volker Endris [ctb], Nicole Pfarr [ctb], Benedikt Brors [ths], Wilko Weichert [ths]

Maintainer: Thomas Wolf <thomas_wolf71 at gmx.de>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("CNVPanelizer")

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("CNVPanelizer")

 

PDF	R Script	CNVPanelizer
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, CopyNumberVariation, Coverage, Normalization, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.2 (R-3.2) (6 years)
License	GPL-3
Depends	R (>= 3.2.0), GenomicRanges
Imports	BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx
LinkingTo
Suggests	knitr, RUnit
SystemRequirements
Enhances
URL
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	CNVPanelizer_1.24.0.tar.gz
Windows Binary	CNVPanelizer_1.24.0.zip
macOS 10.13 (High Sierra)	CNVPanelizer_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNVPanelizer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVPanelizer
Package Short Url	https://bioconductor.org/packages/CNVPanelizer/
Package Downloads Report	Download Stats