Map regulatory landscape across omics
multi-omics-integrationskillsetup L4★35
ammawla/encode-toolkit ↗What it does
Integrate RNA-seq, ChIP-seq, ATAC-seq, DNA methylation across samples for unified view
Best for
Systems understanding of gene regulation when no single modality captures the full biology.
Inputs
- · Expression data (FPKM/TPM)
- · Chromatin states (peaks/calls)
- · Accessibility (ATAC bigWig)
- · Methylation (bedMethyl)
Outputs
- · Chromatin state assignments (active/poised/repressed)
- · Gene activity vs chromatin state correlations
- · Integrative heatmaps
Requires
- · LLM/Claude API
- · Database
- · HTTP/REST API
- · ENCODE/UCSC genomics APIs
- · Git/GitHub
Preconditions
- · All datasets same assembly
- · Sample IDs match across modalities
- · Coverage sufficient for each assay
Failure modes
- · Batch effects across labs/platforms dominate signal
- · Technical replicates mistaken for biological replicates
- · State assignments are assembly/method-specific
Trust signals
- · ENCODE Phase 3 integration pipeline
- · Cites 4D Nucleome consortia