spatial-epigenomics-agent

Core Capabilities

1. Spatial ATAC Analysis: Process spatial chromatin accessibility data to identify open chromatin regions with spatial coordinates.

2. Spatial CUT&Tag: Analyze spatially-resolved histone modification profiles (H3K27ac for enhancers, H3K4me3 for promoters).

3. Spatial Methylation: Map DNA methylation patterns across tissue sections using spatial bisulfite methods.

4. Multi-Modal Integration: Combine spatial epigenomics with spatial transcriptomics for regulatory network inference.

5. Regulatory Element Mapping: Identify spatially-variable enhancers, promoters, and silencers.

6. 3D Chromatin Organization: Integrate with MERFISH/seqFISH+ for spatial chromatin organization.

Technologies Supported

Technology	Epigenetic Mark	Resolution	Method
Spatial-ATAC-seq	Open chromatin	~10-50μm	Microfluidic barcoding
DBiT-seq	ATAC + expression	~10μm	Deterministic barcoding
Spatial-CUT&Tag	Histone marks	~50μm	Cleavage under targets
Spatial-MethylSeq	DNA methylation	Variable	Bisulfite conversion
MERFISH + epigenetics	3D organization	Single-cell	Imaging-based

Workflow

1. Input: Spatial epigenomics data (BAM files + spatial coordinates) or processed peak matrices.

2. Preprocessing: Alignment, deduplication, peak calling with spatial awareness.

3. Spatial Clustering: Identify spatial domains with similar epigenetic profiles.

4. Peak Annotation: Map peaks to genomic features (promoters, enhancers, gene bodies).

5. Motif Analysis: Identify transcription factor binding motifs in spatially-variable peaks.

6. Integration: Combine with expression data for regulatory inference.

7. Output: Spatial peak maps, regulatory networks, domain annotations.