Performance evaluation of Katdetectr and other kataegis detection packages main @ fefbbdc
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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)
# Download the required files into the data/ folder (~1GB).
zen4R::download_zenodo(doi = "10.5281/zenodo.6810477", path = 'data/')
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Creators and SubmitterViews: 1978 Downloads: 180
Created: 7th Jun 2023 at 18:32
Last updated: 7th Jun 2023 at 18:52
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Teams: Katdetectr
Organizations: Erasmus University Medical Centre
https://orcid.org/0000-0002-7513-6813
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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.
Space: Independent Teams
Public web page: https://github.com/ErasmusMC-CCBC/katdetectr
(v.1.16.0-main)