ChAsE

ChAsE visualizes and clusters epigenomic datasets to enable interactive exploration of ChIP-seq-derived chromatin modification and epigenetic marker patterns.

Key Features:

• Interactive visualization: Interactive heat maps and profile plots for dynamic exploration of epigenomic datasets.
• Data clustering: k-means clustering to identify patterns by presence or absence of epigenetic signals, with set operations between clusters for comparative analysis.
• Manual and automatic sorting and brushing: Automatic and manual sorting and brushing within heat maps to refine analyses and focus on specific genomic regions.
• Export capabilities: Export of results and high-quality figures in multiple formats for downstream analysis and publication.

Scientific Applications:

• ChIP-seq epigenomic analysis: Exploration and analysis of ChIP-seq datasets to characterize chromatin modifications.
• Pattern identification: Identification of patterns in chromatin modifications and other epigenetic markers across genomic regions.
• Functional interpretation: Use of clustering and set operations to interpret functional implications of epigenetic states across genomic regions.

Methodology:

Interactive heat maps and profile plots, k-means clustering, set operations between clusters, and manual and automatic sorting and brushing.