motif-scanning
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined by position-specific scoring matrices (PSSMs) from known motif databases. Use this skill when you need to detect the presence and precise genomic coordinates of known TF binding motifs within experimentally defined regions such as ChIP-seq or ATAC-seq peaks.
npx skills add majiayu000/claude-skill-registry --skill 14-toolbased-known-motif-scan-bisnake2001-chromskills-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Motif Scanning ## Overview This skill enables comprehensive motif scanning using HOMER tools for genomic peak files. It scans genomic regions for specific transcription factor binding motifs using position-specific scoring matrices and identifies exact motif locations. To perform motif scanning: - Always refer to the **Inputs & Outputs** section to check inputs and build the output architecture. - Genome assembly: Always returned from user feedback (hg38, mm10, hg19, mm9, etc), never determined by yourself. - Check chromosome names: Standardize chromosome names to format with "chr" (1 -> chr1, MT -> chrM). - Prepare motif files: Position-specific scoring matrices (PSSM) in HOMER format, saved in ${HOMER_data}/knownTFs/motifs/${tf}.motif, and "tf" should be in lower case. - Set scanning parameters: Region size, score thresholds, output format - Run HOMER motif scanning command --- ## When to use this skill - Scan for potential binding sites for a certain TF in the whole genome or in specific genomic regions, like promoters of a gene list or peaks from ChIP-seq or ATAC-seq. - Scanning ChIP-seq or ATAC-seq peaks for known motifs to validate TF binding specificity. - Testing whether
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 0 — Gather Required Information from the User
- Step 1: Initialize Project
- Step 2: Prepare genome file for homer
- Step 3 (Optional): Standardize chromosome names for BED files
- Step 4: Prepare motif file for a certain TF
- Step 5: Scan motif
- Quality Control and Best Practices
- Pre-processing Steps
results/ combined_motifs.txt # combined motif hits from all TFs logs/ # analysis logs motif_scan.log
What does the motif-scanning skill do?
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined by position-specific scoring matrices (PSSMs) from known motif databases. Use this skill when you need to detect the presence and precise genomic coordinates of known TF binding motifs within experimentally defined regions such as ChIP-seq or ATAC-seq peaks.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 14-toolbased-known-motif-scan-bisnake2001-chromskills-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.