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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVPanelizer")
In most cases, you don't need to download the package archive at all.
CNVPanelizer
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Reliable CNV detection in targeted sequencing applications
Bioconductor version: Release (3.4)
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 (from within R,
enter citation("CNVPanelizer")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVPanelizer")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CNVPanelizer")
| R Script | CNVPanelizer | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, CopyNumberVariation, Coverage, Normalization, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.2.0), GenomicRanges |
| Imports | S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr, openxlsx |
| LinkingTo | |
| Suggests | knitr, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CNVPanelizer_1.4.0.tar.gz |
| Windows Binary | CNVPanelizer_1.4.0.zip |
| Mac OS X 10.9 (Mavericks) | CNVPanelizer_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CNVPanelizer/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CNVPanelizer/ |
| Package Downloads Report | Download Stats |
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