HiCaptuRe: An R package for Standarized Processing & Integration of Capture Hi-C Data

HiCaptuRe is an R/Bioconductor package designed to streamline the analysis of capture Hi-C and related chromatin interaction datasets. Unlike existing tools that focus narrowly on statistical modeling or interaction calling, HiCaptuRe provides a standardized framework for data preprocessing, format harmonization, and integration with other omics layers. The package introduces a dedicated object that organizes interaction data together with metadata, enabling reproducible workflows and transparent handling of capture-specific features such as baited versus non-baited fragments. Users can generate bait-centric or region-centric interaction summaries, making the package suitable for linking chromatin contacts with transcriptomic or epigenomic profiles. HiCaptuRe supports multiple input formats, resolves duplicated interactions, and offers functionality for comparative analysis across experimental conditions. By exporting results in widely used formats, it facilitates downstream visualization and integration with external tools. With a modular design and ongoing development, HiCaptuRe fills a critical gap in the Bioconductor ecosystem, providing a capture-aware and integration-ready solution for exploring 3D genome organization and its regulatory impact.Presented at the European Bioconductor Conference (EuroBioC2025), Barcelona, September 2025.