QDNAseq

DOI: 10.18129/B9.bioc.QDNAseq    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see QDNAseq.

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: 3.15

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 "4.2") 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 1.32.0
In Bioconductor since BioC 2.14 (R-3.1) (8.5 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_1.32.0.tar.gz
Windows Binary QDNAseq_1.32.0.zip (64-bit only)
macOS Binary (x86_64) QDNAseq_1.32.0.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

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