katdetectr

DOI: 10.18129/B9.bioc.katdetectr  

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

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Bioconductor version: 3.16

Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.

Author: Daan Hazelaar [aut, cre] , Job van Riet [aut] , Harmen van de Werken [ths]

Maintainer: Daan Hazelaar <daanhazelaar at gmail.com>

Installation

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

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

BiocManager::install("katdetectr")

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("katdetectr")

 

HTML	R Script	Overview_katdetectr
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, SNP, Sequencing, Software, VariantAnnotation, WholeGenome
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2)
Imports	BiocParallel(>= 1.26.2), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomicRanges(>= 1.44.0), GenomeInfoDb(>= 1.28.4), IRanges(>= 2.26.0), maftools(>= 2.10.5), methods (>= 4.1.3), rlang (>= 1.0.2), S4Vectors(>= 0.30.2), tibble (>= 3.1.6), VariantAnnotation(>= 1.38.0), Biobase(>= 2.54.0), Rdpack (>= 2.3.1), ggplot2 (>= 3.3.5), tidyr (>= 1.2.0), BSgenome(>= 1.62.0), ggtext (>= 0.1.1), BSgenome.Hsapiens.UCSC.hg19(>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38(>= 1.4.4), plyranges(>= 1.17.0)
LinkingTo
Suggests	scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/ErasmusMC-CCBC/katdetectr
BugReports	https://github.com/ErasmusMC-CCBC/katdetectr/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	katdetectr_1.0.0.tar.gz
Windows Binary	katdetectr_1.0.0.zip
macOS Binary (x86_64)	katdetectr_1.0.0.tgz
macOS Binary (arm64)	katdetectr_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/katdetectr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/katdetectr
Bioc Package Browser	https://code.bioconductor.org/browse/katdetectr/
Package Short Url	https://bioconductor.org/packages/katdetectr/
Package Downloads Report	Download Stats