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QDNAseq

Quantitative DNA Sequencing for Chromosomal Aberrations


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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

Details

biocViews CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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)
System Requirements
URL https://github.com/ccagc/QDNAseq
Bug Reports https://github.com/ccagc/QDNAseq/issues
See More
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

Package Archives

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

Source Package QDNAseq_1.38.0.tar.gz
Windows Binary QDNAseq_1.38.0.zip
macOS Binary (x86_64) QDNAseq_1.38.0.tgz
macOS Binary (arm64) QDNAseq_1.38.0.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