README.md

In daanhazelaar/katdetectr: Detection, Characterization and Visualization of Kataegis in Sequencing Data

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 Application Note (under submission) 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 foci.
3. Visualization of segmentation and kataegis foci.

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

Not yet published.

Installation

The latest development version can be installed directly from GitHub:

# Require/install devtools package if not already installed.
if (!require("devtools")) install.packages("devtools", repos = "http://cran.r-project.org")

# Install katdetectr from GitHub.
devtools::install_github(repo = "ErasmusMC-CCBC/katdetectr")

# Download all required packages
library(katdetectr)

Or from BioConductor:

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

BiocManager::install("katdetectr")

Usage

Please view the vignettes for instructions and tutorials on how to use this package.

browseVignettes("katdetectr")

daanhazelaar/katdetectr documentation built on June 3, 2022, 4:58 a.m.