De-novo-motif-discovery
This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions of interest such as ChIP-seq peaks, ATAC-seq accessible sites, or differentially acessible regions. It employs HOMER (Hypergeometric Optimization of Motif Enrichment) to detect both known and previously uncharacterized sequence motifs enriched within the supplied genomic intervals. Use the skill when you need to uncover sequence motifs enriched or want to know which TFs might regulate the target regions.
npx skills add majiayu000/claude-skill-registry --skill 12-toolbased-de-novo-motif-discovery --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.
# HOMER De Novo Motif Discovery ## Overview This skill enables comprehensive de novo motif discovery using HOMER tools for genomic peak files. It discovers novel transcription factor binding motifs from genomic regions without requiring prior knowledge of motif patterns. To perform de novo motif discovery: - 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). - Set analysis parameters: Region size, number of motifs, motif lengths - Run HOMER de novo motif discovery command --- ## When to use this skill Use this skill when you need to uncover sequence motifs enriched in the promoter regions of a set of genes, or directly from a set of genomic regions, such as peaks from ChIP-seq or ATAC-seq, without prior assumptions about which transcription factors are involved. Typical use cases include: - Performing motif enrichment analysis in promoters of a gene list provided by user or generated in previous analysis to infer potential
- 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: De Novo Motif Discovery
- Option 1: De novo + known motifs
- Option 2: De novo + known motifs + background
- Option 3: De novo only
results/ homerResults.html # De novo motif discovery results seq.autonorm.tsv # Sequence composition statistics motifFindingParameters.txt # Parameters used for analysis homerMotifs.all.motifs homerMotifs.motifs12 homerMotifs.motifs10 homerMotifs.motifs8 nonRedundant.motifs homerResults/
What does the De-novo-motif-discovery skill do?
This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions of interest such as ChIP-seq peaks, ATAC-seq accessible sites, or differentially acessible regions. It employs HOMER (Hypergeometric Optimization of Motif Enrichment) to detect both known and previously uncharacterized sequence motifs enriched within the supplied genomic intervals. Use the skill when you need to uncover sequence motifs enriched or want to know which TFs might regulate the target regions.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 12-toolbased-de-novo-motif-discovery --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.