multi-omics-integration
multi-omics-integration is a Bioinformatics & life sciences skill for AI agents, published by ammawla in the encode-toolkit repository on GitHub. Skillspace rates multi-omics-integration D (69/100) and it passed the safety scan; the rating is based on static analysis only.
Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.
- Grade
- D
- Quality
- 69 / 100
- Safety
- Passed
- GitHub stars
- 37
Unproven: rated by static analysis only, not yet compared head-to-head.
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Our review
- Architecture
- 90 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- No issues found
- License
- AGPL-3.0
- Adoption
- Adopted by 0 other repositories, in 1 collections
Not checked yet
- Category is a classifier prediction; no model has read this skill yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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