To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("QDNAseq")

In most cases, you don't need to download the package archive at all.

QDNAseq

 

Quantitative DNA sequencing for chromosomal aberrations

Bioconductor version: Release (3.1)

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]

Maintainer: Daoud Sie <d.sie at vumc.nl>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("QDNAseq")

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 1.4.0
In Bioconductor since BioC 2.14 (R-3.1) (1 year)
License GPL
Depends R (>= 2.15.0)
Imports graphics, methods, stats, utils, matrixStats (>= 0.13.1), R.utils (>= 1.28.4), Biobase(>= 2.18.0), CGHbase(>= 1.18.0), CGHcall(>= 2.18.0), DNAcopy(>= 1.32.0), Rsamtools(>= 1.19.17)
LinkingTo
Suggests R.cache (>= 0.9.0), digest, snowfall, BSgenome, GenomeInfoDb
SystemRequirements
Enhances
URL https://github.com/ccagc/QDNAseq
BugReports https://github.com/ccagc/QDNAseq/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source QDNAseq_1.4.0.tar.gz
Windows Binary QDNAseq_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) QDNAseq_1.4.0.tgz
Mac OS X 10.9 (Mavericks) QDNAseq_1.4.0.tgz
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