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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QDNAseq")
In most cases, you don't need to download the package archive at all.
QDNAseq
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see QDNAseq.
Quantitative DNA sequencing for chromosomal aberrations
Bioconductor version: 3.3
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:
## try http:// if https:// URLs are not supported
source("https://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")
| R Script | Introduction to QDNAseq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.8.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (2.5 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 (>= 0.15.0), R.utils (>= 2.2.0), Rsamtools(>= 1.20) |
| LinkingTo | |
| 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) |
| 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 | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | QDNAseq_1.8.1.tar.gz |
| Windows Binary | QDNAseq_1.8.1.zip |
| Mac OS X 10.9 (Mavericks) | QDNAseq_1.8.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/QDNAseq/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/QDNAseq/ |
| Package Downloads Report | Download Stats |
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