DOI: 10.18129/B9.bioc.QDNAseq    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see QDNAseq.

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: 3.10

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")):


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PDF R Script Introduction to QDNAseq
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 2.14 (R-3.1) (6 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 (>= 0.54.0), R.utils (>= 2.9.0), Rsamtools(>= 1.20), future (>= 1.14.0), future.apply (>= 1.3.0)
Suggests BiocStyle(>= 1.8.0), BSgenome(>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb(>= 1.6.0), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10
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
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Source Package QDNAseq_1.22.0.tar.gz
Windows Binary QDNAseq_1.22.0.zip
Mac OS X 10.11 (El Capitan) QDNAseq_1.22.0.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/
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