QDNAseq

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see QDNAseq.

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: 3.16

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], Erik van Dijk [ctb]

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

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

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("QDNAseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("QDNAseq")

Introduction to QDNAseq PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software

Version 1.34.0

In Bioconductor since BioC 2.14 (R-3.1) (10 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 (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools(>= 1.20), future.apply (>= 1.8.1)

System Requirements

URL https://github.com/ccagc/QDNAseq

Bug Reports https://github.com/ccagc/QDNAseq/issues

Suggests BiocStyle(>= 1.8.0), BSgenome(>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb(>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10

Linking To

Enhances

Depends On Me GeneBreak, QDNAseq.hg19, QDNAseq.mm10

Imports Me ACE, biscuiteer, HiCcompare

Suggests Me

Links To Me

Build Report Build Report