tooluniverse-regulatory-genomics
This skill systematically maps gene regulation by integrating transcription factor motifs (JASPAR), experimental ChIP-seq and chromatin data (ENCODE), regulatory variant scoring (RegulomeDB), and sequence-based deep-learning models to predict regulatory activity. Query what controls a gene, whether a variant hits a regulatory element, or how non-coding changes affect expression and accessibility.
tooluniverse-regulatory-genomics identifies transcription factors, binding sites, and regulatory elements affecting genes and genomic regions using integrated databases and deep-learning prediction.
AI-generated summary based on this skill's SKILL.md
Install
mims-harvard/ToolUniverse/tooluniverse-regulatory-genomics · repository language: Python
git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-regulatory-genomics ~/.claude/skills/tooluniverse-regulatory-genomicsFrequently asked questions
AI-generated answers based on this skill's SKILL.md and metadata
What transcription factors bind near my gene using tooluniverse-regulatory-genomics?
tooluniverse-regulatory-genomics identifies transcription factors that bind near your gene by querying JASPAR motifs and integrating ENCODE ChIP-seq experiments. Provide your gene name or genomic coordinates, and the skill maps TF binding sites, shows experimental evidence from multiple cell types, and ranks factors by binding confidence and proximity to regulatory regions.
Does this SNP affect a regulatory element in tooluniverse-regulatory-genomics?
tooluniverse-regulatory-genomics assesses whether your SNP disrupts a regulatory element by annotating the variant's position against known cCREs, ChIP-seq peaks, and ATAC-seq accessible regions. It scores regulatory impact using RegulomeDB-style annotation and predicts whether the variant alters transcription factor binding or chromatin accessibility at that locus.
How can I find CTCF binding sites in liver with tooluniverse-regulatory-genomics?
tooluniverse-regulatory-genomics searches ENCODE ChIP-seq and ATAC-seq experiments for your transcription factor and cell type. Specify CTCF and liver, and the skill returns experimental datasets, peak coordinates, binding strength, and chromatin context. You can filter by cell type, assay type, and tissue to focus on liver-specific regulatory activity.
What enhancers are active in this cell type according to tooluniverse-regulatory-genomics?
tooluniverse-regulatory-genomics identifies active enhancers in your cell type by querying ENCODE ATAC-seq and H3K27ac ChIP-seq data. Provide your cell type and genomic region, and the skill annotates cCREs, maps chromatin accessibility, and highlights enhancers with experimental support. Results include peak coordinates, signal strength, and predicted target genes.
How does tooluniverse-regulatory-genomics predict non-coding variant effects?
tooluniverse-regulatory-genomics predicts non-coding variant regulatory impact by combining sequence-based deep-learning models, TF motif disruption analysis, and RegulomeDB scoring. Input your variant, and the skill forecasts changes to chromatin accessibility, transcription factor binding affinity, and expression effects. Predictions integrate JASPAR motifs and ENCODE experimental context for your cell type.
Can tooluniverse-regulatory-genomics annotate cCREs at specific genomic coordinates?
tooluniverse-regulatory-genomics annotates candidate cis-regulatory elements (cCREs) at your genomic coordinates by integrating ENCODE chromatin data, ChIP-seq peaks, and ATAC-seq accessibility. Provide chromosome, start, and end positions, and the skill classifies regulatory elements by type (promoter, enhancer, silencer), cell type activity, and transcription factor occupancy.
SKILL.md
rendered from the published skill — quoted content, verbatim
Regulatory Genomics Research Skill
Systematic investigation of gene regulation through transcription factor binding, chromatin state, and regulatory element annotation. Integrates JASPAR (TF motifs), ENCODE (functional genomics experiments), RegulomeDB (regulatory variant scoring), and UCSC cCREs.
Domain Reasoning
Regulatory element identification
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skills/tooluniverse-regulatory-genomics/SKILL.md