QDNAseq
This is the development version of QDNAseq; for the stable release version, see QDNAseq.
Quantitative DNA Sequencing for Chromosomal Aberrations
Bioconductor version: Development (3.21)
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("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")| Introduction to QDNAseq | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.43.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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 (>= 0.60.0), 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.
| Source Package | QDNAseq_1.43.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/QDNAseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QDNAseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/QDNAseq/ |
| Package Short Url | https://bioconductor.org/packages/QDNAseq/ |
| Package Downloads Report | Download Stats |