CopywriteR
This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CopywriteR.
Copy number information from targeted sequencing using off-target reads
Bioconductor version: 3.16
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: Oscar Krijgsman <o.krijgsman at nki.nl>
citation("CopywriteR")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CopywriteR")
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("CopywriteR")| CopywriteR | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, ExomeSeq, ImmunoOncology, Preprocessing, Software, TargetedResequencing, Visualization |
| Version | 2.29.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-2 |
| Depends | R (>= 3.2), BiocParallel |
| Imports | matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger |
| System Requirements | |
| URL | https://github.com/PeeperLab/CopywriteR |
See More
| Suggests | BiocStyle, SCLCBam, snow |
| 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 | CopywriteR_2.29.0.tar.gz |
| Windows Binary | CopywriteR_2.30.0.zip |
| macOS Binary (x86_64) | CopywriteR_2.30.0.tgz |
| macOS Binary (arm64) | CopywriteR_2.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CopywriteR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CopywriteR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CopywriteR/ |
| Package Short Url | https://bioconductor.org/packages/CopywriteR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |