ENCODE - sporedata/researchdesigneR GitHub Wiki

General description

The Encyclopedia of DNA Elements (ENCODE) is a public research consortium designed to identify all functional elements in the human and mouse genomes.

ENCODE has over the course of time produced vast amounts of data organized into two levels of annotations:

1. Integrative-level annotations, including a registry of candidate cis-regulatory elements
2. Ground-level annotations derived directly from experimental data.

Related publications

• The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
• Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
• The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state
• A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
• Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations

Data access

For more information, visit the ENCODE Portal.