CNVPanelizer
Reliable CNV detection in targeted sequencing applications
Bioconductor version: 3.24 · Package version: 1.45.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CNVPanelizer")Details
| Maintainer | Thomas Wolf <thomas_wolf71@gmx.de> |
| Author | Cristiano Oliveira [aut], Thomas Wolf [aut, cre], Albrecht Stenzinger [ctb], Volker Endris [ctb], Nicole Pfarr [ctb], Benedikt Brors [ths], Wilko Weichert [ths] |
| License | GPL-3 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, CopyNumberVariation, Coverage, Normalization, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/CNVPanelizer/ |
Citation
From within R, enter citation("CNVPanelizer"):
Cristiano Oliveira, Thomas Wolf. CNVPanelizer: Reliable CNV detection in targeted sequencing applications. doi:10.18129/B9.bioc.CNVPanelizer, R package version 1.45.0, https://bioconductor.org/packages/CNVPanelizer.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CNVPanelizer_1.45.0.tar.gz |
| Windows binary (x86_64) | CNVPanelizer_1.45.0.zip |
| macOS binary (arm64) | CNVPanelizer_1.45.0.tgz |
| macOS binary (x86_64) | CNVPanelizer_1.45.0.tgz |
Dependencies
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