CNVPanelizer
This is the released version of CNVPanelizer; for the devel version, see CNVPanelizer.
Reliable CNV detection in targeted sequencing applications
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.44.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | CNVPanelizer_1.44.0.zip |
| macOS Binary (big-sur-x86_64) | CNVPanelizer_1.44.0.tgz |
| macOS Binary (sonoma-arm64) | CNVPanelizer_1.44.0.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 |