Epigenomics and Chromatin Accessibility Research

NOT for (use other skills instead)

• Methylation array data processing (CpG beta values, differential methylation) -> Use tooluniverse-epigenomics
• RNA-seq differential expression -> Use tooluniverse-rnaseq-deseq2
• GWAS variant interpretation -> Use tooluniverse-gwas-snp-interpretation
• Variant functional annotation from VCF -> Use tooluniverse-variant-analysis

Reasoning: Classify the Question First

Before calling any tool, identify which question type you're answering. Each maps to a different tool set.

(a) Which regulatory elements exist at a locus? Use UCSC_get_encode_cCREs (region-based) or SCREEN_get_regulatory_elements (gene-based). Then check ENCODE_get_chromatin_state for ChromHMM annotation and ENCODE_search_chromatin_accessibility for ATAC-seq evidence.