CNVPanelizer

DOI:10.18129/B9.bioc.CNVPanelizer

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeCNVPanelizer.

Reliable CNV detection in targeted sequencing applications

Bioconductor version: 3.14

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

Installation

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

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

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

Documentation

查看文档的版本包age 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	1.26.0
In Bioconductor since	BioC 3.2 (R-3.2) (6.5 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
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Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	CNVPanelizer_1.26.0.tar.gz
Windows Binary	CNVPanelizer_1.26.0.zip
macOS 10.13 (High Sierra)	CNVPanelizer_1.26.0.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	//www.andersvercelli.com/packages/CNVPanelizer/
Package Downloads Report	Download Stats