# linkSet 0.99.15

## New Features

* Initial Bioconductor submission
* Comprehensive framework for representing, analyzing, and visualizing genomic interactions
* Support for gene-enhancer relationships from Hi-C, PCHi-C, and single-cell ATAC-seq data
* Conversion from common interaction formats (GInteractions, data frames)
* Annotation of promoters and enhancers
* Distance-based analyses and interaction strength metrics
* Statistical modeling using CHiCANE methodology
* Tailored visualization tools for genomic interactions

## Classes and Methods

* `linkSet` class extending GenomicRanges infrastructure
* Methods for subsetting, concatenation, and manipulation of interaction data
* Accessor methods for bait regions, other end regions, and metadata
* Conversion methods to/from GInteractions and data frames

## Analysis Features

* Cross-gene enhancer analysis
* Distance calculations between interacting regions
* Inter/intra-chromosomal interaction classification
* Statistical significance testing with CHiCANE
* Interaction filtering and quality control

## Visualization

* Genomic range plotting with interaction links
* Diagnostic plots for interaction quality assessment
* ggplot2-based visualization framework
* Custom themes for genomic interaction plots

## Documentation

* Comprehensive vignettes with examples
* Complete API documentation
* Integration examples with Bioconductor packages