katdetectr

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see katdetectr.

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Bioconductor version: 3.20

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 "4.4") 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")

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 1.8.0

In Bioconductor since BioC 3.16 (R-4.2) (2.5 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

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

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Package Archives

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

Source Package katdetectr_1.8.0.tar.gz

Windows Binary (x86_64) katdetectr_1.8.0.zip

macOS Binary (x86_64) katdetectr_1.8.0.tgz

macOS Binary (arm64) katdetectr_1.8.0.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/

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