Combine multi-experiment genomic data

Combine multi-omics datasets (genomics, epigenomics, transcriptomics)

Creating a coherent multi-layer view of gene regulation by integrating ENCODE with expression, variation, and protein data

• · ENCODE peaks
• · RNA-seq TPM
• · variant calls
• · protein data

• · unified dataset
• · cross-omics correlations
• · integrated report

• · R/Python integrative frameworks
• · bedtools
• · GenomicRanges

Matched sample metadata across all omics layers

• · Batch effects across platforms
• · Missing sample overlap
• · Integration assumptions violated

• · Multi-omics coordination
• · Cross-platform normalization