encode-databaselisted

# ENCODE Database ## Overview The ENCODE (Encyclopedia of DNA Elements) Project has generated thousands of functional genomics experiments — TF ChIP-seq, ATAC-seq, DNase-seq, histone ChIP-seq, and RNA-seq — across 1000+ human and mouse cell types and tissues. The ENCODE Portal REST API provides structured JSON access to experiment metadata, file download URLs, and SCREEN cCRE (candidate cis-Regulatory Elements) annotations. All data is freely accessible without authentication for most endpoints. ## When to Use - Downloading TF ChIP-seq peak files (BED) for a specific transcription factor and cell type to annotate regulatory regions - Finding ATAC-seq or DNase-seq peaks in a cell type to identify open chromatin regions near a gene of interest - Retrieving cCREs (candidate cis-Regulatory Elements) overlapping a genomic region from ENCODE SCREEN - Building reference regulatory tracks for variant annotation pipelines (e.g., annotating VCF variants against ENCODE peak sets) - Exploring which experiments are available for a biosample (cell line, tissue, developmental stage) before planning a wet-lab experiment - Querying all ChIP-seq experiments for a transcription factor across multiple cell types for comparative regulatory analysis - Use `regulomedb-database` instead when you want pre-computed regulatory scores for specific SNPs — RegulomeDB integrates ENCODE data with eQTL and motif evidence into a single score - Use `deeptools-ngs-analysis` instead when you have your own BA