ArticleBMC genomics2021
kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study.Genome medicine · 2026Observational
- Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study.Research square · 2025Article
- Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.Nature communications · 2025Article
- Kataegis associated mutational processes linked to adverse prostate cancer presentation in African men.Research square · 2024Article
- HotSPOT: A Computational Tool to Design Targeted Sequencing Panels to Assess Early Photocarcinogenesis.Cancers · 2023Article
- Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection.GigaScience · 2022Article
- Examining clustered somatic mutations with SigProfilerClusters.Bioinformatics (Oxford, England) · 2022Article
- Cancer Cytogenetics: Deep Roots, New Branches in the Age of Omics.Cancer genomics & proteomicsReview
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Authors and funding
10 authors.
Funding
Abstract
backgroundGenomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations "violent storm", which is just what the Greek word "kataegis" means.
resultsThere are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package "kataegis" to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions.
conclusionsThe kataegis package is available on Bionconductor/Github ( https://github.com/flosalbizziae/kataegis ), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.
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