Home
Bioconductor 3.23
Software Packages
katdetectr (development version)

katdetectr

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

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.katdetectr

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0002-7513-6813 , Job van Riet [aut] ORCID iD ORCID: 0000-0001-7767-7923 , Harmen van de Werken [ths] ORCID iD ORCID: 0000-0002-9794-1477

Maintainer: Daan Hazelaar <daanhazelaar at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

Overview_katdetectr HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, SNP, Sequencing, Software, VariantAnnotation, WholeGenome

Version 1.13.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License GPL-3 + file LICENSE

Depends R (>= 4.2)

Imports Biobase(>= 2.54.0), BiocParallel(>= 1.26.2), BSgenome(>= 1.62.0), BSgenome.Hsapiens.UCSC.hg19(>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38(>= 1.4.4), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomeInfoDb(>= 1.28.4), GenomicRanges(>= 1.44.0), ggplot2 (>= 3.3.5), ggtext (>= 0.1.1), IRanges(>= 2.26.0), maftools(>= 2.10.5), methods (>= 4.1.3), plyranges(>= 1.17.0), Rdpack (>= 2.3.1), rlang (>= 1.0.2), S4Vectors(>= 0.30.2), scales (>= 1.2.0), tibble (>= 3.1.6), tidyr (>= 1.2.0), tools, utils, VariantAnnotation(>= 1.38.0)

System Requirements

URL https://doi.org/doi:10.18129/B9.bioc.katdetectr

Bug Reports https://github.com/ErasmusMC-CCBC/katdetectr/issues

See More

Suggests BiocStyle(>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package katdetectr_1.13.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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