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>

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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)
Suggests scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0)
URL https://github.com/ErasmusMC-CCBC/katdetectr
BugReports https://github.com/ErasmusMC-CCBC/katdetectr/issues
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