{"enrichment":{"faq":[{"a":"tooluniverse-epigenomics-chromatin integrates histone ChIP-seq datasets to reveal histone mark patterns (H3K27ac, H3K4me3, and others) across genomic loci. You can query specific regions to identify active promoters, enhancers, and repressed chromatin states, then compare histone modification landscapes across tissues using Roadmap Epigenomics and ENCODE data for comprehensive chromatin state assessment.","q":"How does tooluniverse-epigenomics-chromatin enable histone modifications ChIP-seq analysis?"},{"a":"tooluniverse-epigenomics-chromatin helps identify transcription factor binding sites, ENCODE cCRE regulatory elements, enhancers, promoters, and bivalent promoters. You can map cis-regulatory element annotations and explore ChIP-Atlas transcription factor binding patterns to build a complete regulatory landscape view at your genomic region of interest.","q":"What regulatory elements can I identify with this skill?"},{"a":"Yes. tooluniverse-epigenomics-chromatin supports regulatory variant interpretation by overlaying variant positions against histone marks, chromatin accessibility peaks, transcription factor binding sites, and eQTL associations. This multi-layer evidence synthesis reveals whether variants fall in active regulatory regions and their potential cis-regulatory impact.","q":"Can tooluniverse-epigenomics-chromatin assess how non-coding variants affect regulation?"},{"a":"tooluniverse-epigenomics-chromatin provides tissue-specific ATAC-seq chromatin accessibility data and DNase accessibility peaks. Query your region of interest to retrieve open chromatin signatures across different cell types and tissues, enabling you to compare accessibility patterns and identify tissue-specific regulatory activity.","q":"How do I map chromatin accessibility and ATAC-seq data by tissue?"},{"a":"tooluniverse-epigenomics-chromatin queries eQTLs (expression quantitative trait loci) and tissue-specific gene regulation patterns. You can investigate how genetic variants associate with gene expression changes across tissues and integrate these associations with chromatin state data to understand regulatory mechanisms.","q":"What eQTL and gene regulation features does this skill offer?"},{"a":"tooluniverse-epigenomics-chromatin draws from ENCODE, Roadmap Epigenomics, and ChIP-Atlas. These resources provide comprehensive histone modification maps, chromatin accessibility data, regulatory element annotations, and transcription factor binding information across diverse cell types and tissues under the Apache-2.0 license.","q":"Which data sources power tooluniverse-epigenomics-chromatin?"}],"shadow_tags":["chip-seq-analysis","chromatin-accessibility","regulatory-elements","histone-marks","transcription-factors","eqtl-mapping","enhancer-discovery","epigenetic-landscape","variant-scoring","gene-regulation"],"summary_rewrite":"Access histone ChIP-seq data, chromatin accessibility maps, and regulatory element annotations from ENCODE and Roadmap Epigenomics to investigate chromatin state by tissue, transcription factor binding patterns, and cis-regulatory landscapes. Interpret histone marks, eQTL associations, and variant regulatory impact through multi-layer evidence synthesis."},"files":[{"bytes":13384,"path":"skills/tooluniverse-epigenomics-chromatin/SKILL.md","sha256":"01ad83c1a5cd269e0a1085afe680a9f203bbfabab625a3c9468ce292b6ff7db0","url":"https://skillfed.io/files/mims-harvard/ToolUniverse/tooluniverse-epigenomics-chromatin/b4dafaa7/SKILL.md"}],"id":"mims-harvard/ToolUniverse/tooluniverse-epigenomics-chromatin","links":{"html":"https://skillfed.io/mims-harvard/ToolUniverse/tooluniverse-epigenomics-chromatin","md":"https://skillfed.io/mims-harvard/ToolUniverse/tooluniverse-epigenomics-chromatin.md","repo":"https://github.com/mims-harvard/ToolUniverse"},"meta":{"agents_supported":[],"first_seen":"2026-07-28","forks":242,"language":"Python","last_updated":"2026-07-27","license":"Apache-2.0","name":"tooluniverse-epigenomics-chromatin","publisher":"mims-harvard","stars":1595},"relations":{"similar":[{"id":"mims-harvard/ToolUniverse/tooluniverse-regulatory-genomics"},{"id":"mims-harvard/ToolUniverse/tooluniverse-gene-regulatory-networks"},{"id":"jaechang-hits/SciAgent-Skills/encode-database"},{"id":"mims-harvard/ToolUniverse/tooluniverse-regulatory-variant-analysis"},{"id":"jaechang-hits/SciAgent-Skills/macs3-peak-calling"},{"id":"jaechang-hits/SciAgent-Skills/regulomedb-database"},{"id":"mims-harvard/ToolUniverse/tooluniverse-variant-to-mechanism"},{"id":"LeonChaoX/qinyan-academic-skills/jaspar-database"},{"id":"google-deepmind/science-skills/encode_ccres_database"},{"id":"mims-harvard/ToolUniverse/tooluniverse-epigenomics"}]},"slug":{"owner":"mims-harvard","repo":"ToolUniverse","skill":"tooluniverse-epigenomics-chromatin"},"version":"b4dafaa7"}