QDNAseq

This is the released version of QDNAseq; for the devel version, see QDNAseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: Release (3.23)

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>

Citation (from within R, enter citation("QDNAseq")):

Ilari Scheinin, Daoud Sie, Henrik Bengtsson. QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations. doi:10.18129/B9.bioc.QDNAseq, R package version 1.48.0, https://bioconductor.org/packages/QDNAseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Introduction to QDNAseq	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software
Version	1.48.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	GPL
Depends	R (>= 3.1.0)
Imports	graphics, methods, stats, utils, BiocGenerics, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), Seqinfo, GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1)
System Requirements
URL	https://github.com/ccagc/QDNAseq
Bug Reports	https://github.com/ccagc/QDNAseq/issues

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
Linking To
Enhances
Depends On Me	GeneBreak, QDNAseq.hg19, QDNAseq.mm10
Imports Me	ACE, biscuiteer, cfdnakit
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	QDNAseq_1.48.0.tar.gz
Windows Binary (x86_64)	QDNAseq_1.48.0.zip
macOS Binary (big-sur-x86_64)	QDNAseq_1.48.0.tgz
macOS Binary (sonoma-arm64)	QDNAseq_1.48.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QDNAseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QDNAseq
Package Short Url	https://bioconductor.org/packages/QDNAseq/
Package Downloads Report	Download Stats