QDNAseq

DOI: 10.18129/B9.bioc.QDNAseq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see QDNAseq.

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: 3.16

Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Author: Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut], Erik van Dijk [ctb]

Maintainer: Daoud Sie <d.sie at vumc.nl>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QDNAseq")

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("QDNAseq")

 

PDF	R Script	Introduction to QDNAseq
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software
Version	1.34.0
In Bioconductor since	BioC 2.14 (R-3.1) (9 years)
License	GPL
Depends	R (>= 3.1.0)
Imports	graphics, methods, stats, utils, Biobase(>= 2.18.0), CGHbase(>= 1.18.0), CGHcall(>= 2.18.0), DNAcopy(>= 1.32.0), GenomicRanges(>= 1.20), IRanges(>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools(>= 1.20), future.apply (>= 1.8.1)
LinkingTo
Suggests	BiocStyle(>= 1.8.0), BSgenome(>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb(>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10
SystemRequirements
Enhances
URL	https://github.com/ccagc/QDNAseq
BugReports	https://github.com/ccagc/QDNAseq/issues
Depends On Me	GeneBreak, QDNAseq.hg19, QDNAseq.mm10
Imports Me	ACE, biscuiteer, HiCcompare
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	QDNAseq_1.34.0.tar.gz
Windows Binary	QDNAseq_1.34.0.zip
macOS Binary (x86_64)	QDNAseq_1.34.0.tgz
macOS Binary (arm64)	QDNAseq_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QDNAseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QDNAseq
Bioc Package Browser	https://code.bioconductor.org/browse/QDNAseq/
Package Short Url	https://bioconductor.org/packages/QDNAseq/
Package Downloads Report	Download Stats