katdetectr

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Bioconductor version: 3.23 · Package version: 1.14.0

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.

Installation

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

BiocManager::install("katdetectr")

Details

Maintainer	Daan Hazelaar <daanhazelaar@gmail.com>
Author	Daan Hazelaar [aut, cre] (ORCID: <https://orcid.org/0000-0002-7513-6813>), Job van Riet [aut] (ORCID: <https://orcid.org/0000-0001-7767-7923>), Harmen van de Werken [ths] (ORCID: <https://orcid.org/0000-0002-9794-1477>)
License	GPL-3 + file LICENSE
URL	https://doi.org/doi:10.18129/B9.bioc.katdetectr
Bug Reports	https://github.com/ErasmusMC-CCBC/katdetectr/issues
Downloads rank	259
Source branch	RELEASE_3_23
biocViews	Classification, SNP, Sequencing, Software, VariantAnnotation, WholeGenome

Documentation

Overview of katdetectr

Download

Source package

Dependencies

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)

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