Overview | Importing Interaction Data: load_interactions() | What is a HiCaptuRe object? | Inspecting the HiCaptuRe Object | Tracking Parameters Used in Each Step | Digesting the Genome: digest_genome() | Enzyme Parameters | Controlling Genome Digestion | Performance and Caching | Annotating Interactions: annotate_interactions() | Filtering Interactions | Filtering interactions by Baits of interest: interactionsByBaits() | Bait Summary: getByBaits() | Filtering by Genomic Regions: interactionsByRegions() | Regions Summary: getByRegions() | Intersecting Interaction Sets: intersect_interactions() | Summarizing Interaction Distances: distance_summary | Visualizing Distance Distributions: plot_distance_summary() | Extracting Interactions from a peakmatrix: peakmatrix2list() | Exporting Processed Interaction Data: export_interactions() | SessionInfo

Installation | Overview | Motivation for Bioconductor | Basic Vocabulary | Data Origin and Experimental Workflow | Capture Hi-C Data Formats (some CHiCAGO outputs) | interBed - ibed — Recommended Format | peakmatrix — Multi-sample Interaction Matrix | seqMonk — Two-row Interaction Format | **bedpe ** — Generic Paired-End Interaction Format | **washU ** — Minimal Format for Browser Upload | **washUold ** — (Legacy) | Summary | The HiCaptuRe Object | Typical Workflow | Example Data | 📚 References | SessionInfo