katdetectr

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 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:

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

BiocManager::install("katdetectr")

Development version

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("https://github.com/ErasmusMC-CCBC/katdetectr")