GenomicDistributions

GenomicDistributions provides R functions to compute summary statistics and generate ggplot-based visualizations of genomic region sets from assays such as ChIP-seq and ATAC-seq to support analyses of gene regulation and epigenomic landscapes.

Key Features:

• Comprehensive statistical analysis: Calculates properties of genomic regions including feature distances, overlaps with genomic partitions, and other region-level statistics.
• Assay support: Handles region sets derived from assays such as ChIP-seq and ATAC-seq.
• Optimized performance: Functions are optimized for speed to enable rapid processing of large genomic region sets.
• Visualization capabilities: Provides plotting functions that generate editable ggplot objects for customizable figures.
• Flexible input handling: Accepts both single and multiple region set inputs for analysis.
• Scalability: Built to scale with increasing data volumes typical of epigenomics datasets.

Scientific Applications:

• Gene regulation studies: Characterizes spatial organization and overlaps of genomic regions to inform regulatory mechanism analyses.
• Exploratory epigenomic analysis: Summarizes and visualizes region-set properties to support hypothesis generation and exploratory data analysis.
• Epigenomic landscape interpretation: Enables comparison and visualization of region distributions across samples or genomic partitions to aid interpretation of complex epigenomic datasets.

Methodology:

Calculations include feature distance metrics and overlaps with genomic partitions; functions are optimized for speed to rapidly process large genomic region sets, and plotting functions return editable ggplot objects.