kataegis

kataegis identifies localized hypermutation (kataegis) regions in cancer genomes by analyzing mutation coordinates and visualizing nucleotide contexts to characterize clustered somatic mutations.

Key Features:

• R package: Implemented as an R package for analysis of genomic mutation data.
• Input handling: Reads variation files formatted according to standard genomic data specifications.
• Inter-mutational distance calculation: Computes inter-mutational distances to assess the spatial distribution of mutations.
• Kataegis detection: Identifies localized hypermutation regions (kataegis) using customizable parameters.
• Visualization of nucleotide context: Visualizes nucleotide contents and mutation spectra within identified foci and in adjacent flanking regions.
• Three-step workflow: Operates via a three-step process of reading data, calculating distances, and detecting hypermutation regions.

Scientific Applications:

• Kataegis identification: Detection and characterization of clustered somatic mutation regions in cancer genomes.
• Mutation spectrum analysis: Examination of nucleotide contents and mutation spectra within hypermutation foci and flanking sequences.
• Cancer research: Analysis of localized hypermutation to inform studies of mutation processes and potential implications for cancer prognosis.

Methodology:

Reads variation files, calculates inter-mutational distances, detects hypermutation regions using customizable parameters, and generates visualizations of nucleotide contents and mutation spectra within foci and flanking regions.