search-encodelisted

# Search ENCODE Data ## When to Use - User wants to find ENCODE experiments matching specific criteria (assay, organ, cell type, target) - User asks "what ENCODE data exists for [tissue/target/assay]?" - User wants to explore available data before downloading - User needs to find specific file types (BED, BAM, bigWig) across experiments - User wants to know how many experiments exist for a condition - User asks about available assays, organisms, or biosamples in ENCODE Help the user find ENCODE experiments and files. Use the appropriate tools based on what they need. ## Search Strategy 1. **Finding experiments**: Use `encode_search_experiments` with filters: - `assay_title`: "Histone ChIP-seq", "ATAC-seq", "RNA-seq", "TF ChIP-seq", "Hi-C", "CUT&RUN", "WGBS", etc. - `organ`: "pancreas", "brain", "liver", "heart", "kidney", "lung", etc. - `biosample_type`: "tissue", "cell line", "primary cell", "organoid" - `biosample_term_name`: specific name like "GM12878", "HepG2", "K562" - `target`: ChIP/CUT&RUN target like "H3K27me3", "H3K4me3", "CTCF", "p300" - `organism`: "Homo sapiens" (default) or "Mus musculus" 2. **Finding files across experiments**: Use `encode_search_files` when the user wants specific file types from multiple experiments. 3. **Exploring available data**: Use `encode_get_facets` to see counts of what exists before searching. Use `encode_get_metadata` to list valid filter values. 4. **Getting experiment details**: Use `encode_get_experiment