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Bioconductor - QDNAseq (development version)

QDNAseq

This is the development version of QDNAseq; for the stable release version, see QDNAseq.

Quantitative DNA Sequencing for Chromosomal Aberrations

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software Version 1.45.0 In Bioconductor since BioC 2.14 (R-3.1) (11 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 See More 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, cfdnakit Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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