Bioconductor Code: katdetectr (original) (raw)

# katdetectr  [\](https://github.com/ErasmusMC-CCBC/katdetectr/issues)  ## Introduction `katdetectr` is an *R* package for the detection, characterization and visualization of localized hypermutated regions, often referred to as *kataegis*. Please see the [Technical Note](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad081/7319580) for additional background, details and performance evaluations of `katdetectr`. The general workflow of `katdetectr` can be summarized as follows: 1. Import of genomic variants; VCF, MAF or VRanges objects. 2. Detection of kataegis loci. 3. Visualization of segmentation and kataegis loci. Please see the vignette for an overview of the workflow in a step-by-step manner on publicly-available datasets which are included within this package. ## Citation Hazelaar, D. M., van Riet, J., Hoogstrate, Y., & van de Werken, H. J. (2023). Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection. GigaScience, 12, giad081. ## Installation Download katdetectr from BioConductor or Github: ```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("katdetectr") ``` ### Development version ```R if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("https://github.com/ErasmusMC-CCBC/katdetectr") ```