Annotate chromatin loops with regulatory features from bedpe inputs using HOMER.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill loop-annotation
Please help me install this Agent Skill. Skill: loop-annotation Source: https://github.com/BIsnake2001/ChromSkills/tree/main/33.loop-annotation Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill loop-annotation
This skill annotates chromatin loops for Hi-C/HiChIP/ChIA-PET data, assigning enhancers, promoters, and CTCF overlaps, and can auto-create missing enhancer and promoter sets for complete loop context.
Provide the required inputs (loops.bedpe, ctcf_peaks.bed, and genome) and run the loop-annotation workflow to generate annotated loop categories and visualizations.
High-intent search queries and answers about installing and using this skill.
To annotate chromatin loops, provide loops.bedpe, ctcf_peaks.bed, and a genome identifier. The workflow uses HOMER and annotateInteractions.pl to categorize loop types and map regulatory overlaps.
Categorizing chromatin loops requires a loops.bedpe file, a ctcf_peaks.bed file, and a genome identifier. These inputs drive the HOMER-based annotation pipeline to map regulatory features.
Yes, you can build missing enhancers.bed and promoters.bed sets if they are absent. The workflow auto-creates them using ATAC/H3K27ac signals and gene annotations for complete loop context.
Yes, the loop annotation workflow generates visualizations. It produces standardized plots of annotated loop categories to support downstream regulatory loop analyses.
To standardize bedpe inputs for HiChIP data, the workflow processes the raw loops.bedpe file to format it correctly for downstream HOMER-based annotation and feature categorization.
BIsnake2001Identify enriched transcription factor motifs in genomic regions using HOMER.
ammawlaRetrieve GTEx median TPM values to validate ENCODE regulatory findings.
ammawlaAggregate Hi-C loop calls from multiple experiments into a union chromatin contact catalog.
LeonChaoXScan DNA sequences for transcription factor binding sites using JASPAR PWM profiles.
