Katdetectr
OverviewKataegis 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.
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SEEK ID: https://workflowhub.eu/projects/162
Public web page: https://github.com/ErasmusMC-CCBC/katdetectr
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Team created: 26th Apr 2023
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Teams: Katdetectr
Organizations: Erasmus University Medical Centre
https://orcid.org/0000-0002-7513-6813
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Introduction
This repository contains all the custom scripts used in the evaluation and comparison of Katdetectr as described in the corresponding Technical Note (under submission).
Usage
All required files were deposited on Zenodo.
These can directly be downloaded using zen4R and be used as input.
# Increase the timeout (due to some large files).
options(timeout=5000)
...
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:
- Import of genomic variants; VCF, MAF or VRanges objects.
- Detection ...
