QDNAseq-package: Package QDNAseq
In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations
QDNAseq-package R Documentation
Package QDNAseq
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.
Details
A package to detect chromosomal aberrations from whole-genome sequencing
data. QDNAseqReadCounts and QDNAseqCopyNumbers classes are
used as the main data structures.
How to cite this package
Whenever using this package, please cite:
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl
HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC,
Wesseling P, Pinkel D, Albertson DG, Ylstra B (2014). "DNA copy number
analysis of fresh and formalin-fixed specimens by shallow whole-genome
sequencing with identification and exclusion of problematic regions in
the genome assembly." _Genome Research_, *24*, 2022-2032.
License
This package is licensed under GPL.
Author(s)
Ilari Scheinin
ccagc/QDNAseq documentation built on July 28, 2024, 3:46 p.m.
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| QDNAseq-package | R Documentation |
Package QDNAseq
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.
Details
A package to detect chromosomal aberrations from whole-genome sequencing
data. QDNAseqReadCounts and QDNAseqCopyNumbers classes are
used as the main data structures.
How to cite this package
Whenever using this package, please cite: Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B (2014). "DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly." _Genome Research_, *24*, 2022-2032.
License
This package is licensed under GPL.
Author(s)
Ilari Scheinin
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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