This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CopywriteR.
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 (from within R,
enter citation("CopywriteR")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CopywriteR")
R Script | CopywriteR | |
Reference Manual | ||
Text | NEWS |
biocViews | CopyNumberVariation, Coverage, ExomeSeq, ImmunoOncology, Preprocessing, Software, TargetedResequencing, Visualization |
Version | 2.29.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (8 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 |
LinkingTo | |
Suggests | BiocStyle, SCLCBam, snow |
SystemRequirements | |
Enhances | |
URL | https://github.com/PeeperLab/CopywriteR |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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 |
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