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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: 3.0
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.
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")
| R Script | Introduction to QDNAseq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.2.4 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL |
| Depends | R (>= 2.15.0) |
| Imports | graphics, methods, stats, utils, matrixStats (>= 0.9.4), R.utils (>= 1.28.4), Biobase(>= 2.18.0), CGHbase(>= 1.18.0), CGHcall(>= 2.18.0), DNAcopy(>= 1.32.0), Rsamtools(>= 1.10.0) |
| LinkingTo | |
| Suggests | R.cache (>= 0.9.0), digest, snowfall, BSgenome, GenomeInfoDb |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/ccagc/QDNAseq |
| 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_1.2.4.tar.gz |
| Windows Binary | QDNAseq_1.2.4.zip |
| Mac OS X 10.6 (Snow Leopard) | QDNAseq_1.2.4.tgz |
| Mac OS X 10.9 (Mavericks) | QDNAseq_1.2.4.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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