StatePaintR

StatePaintR generates chromatin state annotations from combinatorial epigenomic models to support genome annotation and interpretation of disease-associated variants.

Key Features:

• Combinatorial Epigenomic Model: Defines chromatin states using combinatorial epigenomic models derived from epigenetic data.
• Integration with Bioconductor: Implements annotation workflows within the Bioconductor ecosystem.
• Rapid Chromatin Segmentation: Produces chromatin state segmentations in standard genome browser formats in seconds.
• Quantitative Analysis Capabilities: Calculates ranks for each chromatin state from next-generation sequencing peak statistics to support variant prioritization and enrichment testing.
• Resource Hub - StateHub: Leverages StateHub as a repository of annotation tracks from Roadmap, ENCODE, Blueprint, CEEHRC, and DEEP and accepts alternative models.

Scientific Applications:

• Genome Annotation: Annotates genomes with chromatin state maps to inform regulatory element identification.
• Variant Interpretation: Prioritizes and interprets disease-associated variants using ranked chromatin state information in clinical and research contexts.
• Epigenetic Regulation Analysis: Facilitates interpretation of epigenetic data for gene regulation and expression analyses.
• Comparative and Meta-Analyses: Enables comparative analyses and meta-analyses by leveraging consortia annotation tracks.

Methodology:

Defines chromatin states from combinatorial epigenomic models, calculates ranks per state from next-generation sequencing peak statistics, and outputs chromatin state segmentations in standard genome browser formats via Bioconductor and StateHub annotation tracks.