epistack

epistack visualizes stacks of genomic tracks centered at genomic regions of interest for integrative epigenomic analysis.

Key Features:

• Multi-assay compatibility: Supports visualization of ChIP-seq, ATAC-seq, DNA methylation, and genomic conservation data.
• GRanges-based input: Accepts genomic score objects as GRanges from bigwig or bam files.
• Feature-centered alignment: Centers tracks on regions of interest such as peaks or transcription start sites provided as GRanges from gtf or bed files.
• Feature sorting: Sorts features by a user-provided score such as peak height or gene expression value.

Scientific Applications:

• Epigenomic profiling: Generates heatmaps of stack profiles from epigenetic signals around genomic features.
• Integrative epigenomics: Enables comparison of multiple epigenetic marks and genomic features in a unified visualization framework.

Methodology:

epistack takes three inputs—genomic score objects as GRanges, features of interest as GRanges, and a sorting score—to produce centered, stacked visualizations of genomic tracks.