QDNAseq

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: 3.23 · Package version: 1.48.0

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.

Installation

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

BiocManager::install("QDNAseq")

Details

Maintainer	Daoud Sie <d.sie@vumc.nl>
Author	Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut], Erik van Dijk [ctb]
License	GPL
URL	https://github.com/ccagc/QDNAseq
Bug Reports	https://github.com/ccagc/QDNAseq/issues
Downloads rank	761
Source branch	RELEASE_3_23
biocViews	CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software

Documentation

Introduction to QDNAseq

Download

Source package

Dependencies

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)

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

Reverse dependencies

Depends On Me (3): GeneBreak, QDNAseq.hg19, QDNAseq.mm10

Imports Me (3): ACE, biscuiteer, cfdnakit