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Package: QDNAseq
Version: 1.8.0
Date: 2016-03-22
Title: Quantitative DNA sequencing for chromosomal aberrations
Author: Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut]
Maintainer: Daoud Sie <d.sie@vumc.nl>
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 (>=
0.15.0), R.utils (>= 2.2.0), Rsamtools (>= 1.20),
Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>=
0.6.8), GenomeInfoDb (>= 1.6.0), future (>= 0.12.0), R.cache
(>= 0.12.0)
Description: 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.
biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
Preprocessing, QualityControl, Sequencing
License: GPL
URL: https://github.com/ccagc/QDNAseq
BugReports: https://github.com/ccagc/QDNAseq/issues
NeedsCompilation: no
Packaged: 2016-05-04 05:22:15 UTC; biocbuild
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providing 
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