Package index
Module 1: Data Consolidation & Preprocessing
Foundational data-cleaning engine for merging and standardizing 3D interactomes.
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consolidate_chromatin_loops() - Consolidate and Integrate Chromatin Loops from Multiple Sources
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bedpe_to_gi() - Read BEDPE File into a GInteractions Object
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reduce_ginteractions() - Spatial Clustering of GInteractions
Module 2: 3D-Guided Peak Annotation
The core mapping engine for resolving 1D-to-3D spatial target assignments.
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annotate_peaks_and_loops() - A core analytical engine enabling high-resolution spatial mapping of genomic features/peaks to 3D chromatin interaction targets
Module 3: Expression-Aware Refinement
Advanced logic for eliminating transcriptionally silent contacts using RNA-seq data.
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refine_loop_anchors_by_expression() - A transcriptome-informed filtering framework to refine the regulatory element (anchor) classification and the loop-target linkage using gene expression profiles
Module 4: Automated Functional Profiling
End-to-end integration with JASPAR motifs, GO enrichment, and PPI networks.
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profile_target_genes() - End-to-end functional annotation pipeline integrating JASPAR transcription factor motif analysis, gene ontology enrichment, and protein-protein interaction network analysis
Module 5: IGV-Style & Statistical Visualization
Publication-ready tools for rendering genomic tracks and statistical summaries.
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plot_peaks_interactions() - Publication-ready visualization toolkit for rendering genomic track data and statistical summaries related to 3D chromatin interactions
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draw_flower_simplified() - Draw Simplified Flower Plot for Core vs. Unique Genes
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draw_upset_intersections() - Generate UpSet Plot for Gene Set Intersections
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read_simple_bed() - Read a Simple BED File into a GRanges Object