Individual skill
tooluniverse-epigenomics-chromatin
Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas. Use for chromatin-state-by-tissue queries, TF-binding-by-region, regulatory landscape mapping, and ENCODE-cCRE annotations. For DNA methylation use tooluniverse-epigenomics; for RNA-seq use tooluniverse-rnaseq-deseq2.
plugins/tooluniverse/skills/tooluniverse-epigenomics-chromatin/SKILL.md
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- Apache-2.0
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# 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.