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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("CopywriteR")
In most cases, you don't need to download the package archive at all.
CopywriteR
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see CopywriteR.
Copy number information from targeted sequencing using off-target reads
Bioconductor version: 3.2
CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.
Author: Thomas Kuilman
Maintainer: Thomas Kuilman <t.kuilman at nki.nl>
Citation (from within R,
enter citation("CopywriteR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CopywriteR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CopywriteR")
| CopywriteR | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Coverage, ExomeSeq, Preprocessing, Software, TargetedResequencing, Visualization |
| Version | 2.2.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (1 year) |
| License | GPL-2 |
| Depends | R (>= 3.2), BiocParallel |
| Imports | matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger |
| LinkingTo | |
| Suggests | BiocStyle, SCLCBam, snow |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/PeeperLab/CopywriteR |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CopywriteR_2.2.0.tar.gz |
| Windows Binary | CopywriteR_2.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CopywriteR_2.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | CopywriteR_2.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CopywriteR/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/CopywriteR/ |
| Package Downloads Report | Download Stats |
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