CNVPanelizer
Reliable CNV detection in targeted sequencing applications
Bioconductor version: Release (3.20)
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>
citation("CNVPanelizer")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| CNVPanelizer | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, CopyNumberVariation, Coverage, Normalization, Sequencing, Software |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.2.0), GenomicRanges |
| Imports | BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx |
| System Requirements | |
| URL |
See More
| Suggests | knitr, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CNVPanelizer_1.38.0.tar.gz |
| Windows Binary (x86_64) | CNVPanelizer_1.38.0.zip |
| macOS Binary (x86_64) | CNVPanelizer_1.38.0.tgz |
| macOS Binary (arm64) | CNVPanelizer_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNVPanelizer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNVPanelizer |
| Bioc Package Browser | https://code.bioconductor.org/browse/CNVPanelizer/ |
| Package Short Url | https://bioconductor.org/packages/CNVPanelizer/ |
| Package Downloads Report | Download Stats |