bio-chipseq-motif-analysis
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
npx skills add majiayu000/claude-skill-registry --skill motif-analysis-gptomics-bioskills-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 Analysis Identify DNA sequence motifs enriched in ChIP-seq or ATAC-seq peaks to discover transcription factor binding sites. ## Tool Comparison | Tool | Strengths | Use Case | |------|-----------|----------| | HOMER | Fast, comprehensive, built-in databases | General motif analysis | | MEME-ChIP | Multiple algorithms, web interface | Publication-quality | | MEME | De novo discovery only | Simple discovery | | FIMO | Known motif scanning | Genome-wide scanning | ## HOMER ### Installation ```bash conda install -c bioconda homer # Configure genome (required once) perl /path/to/homer/configureHomer.pl -install hg38 perl /path/to/homer/configureHomer.pl -install mm10 ``` ### De Novo Motif Discovery ```bash # Basic motif finding findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 # With background regions findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 -bg background.bed # Specify motif lengths to search findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 -len 8,10,12 ``` ### Key Options | Option | Description | |--------|-------------| | `-size <#>` | Fragment size for analysis (default 200) | | `-size given` | Use actual peak sizes | | `-bg <file>` | Backgrou
- Tool Comparison
- HOMER
- Installation
- De Novo Motif Discovery
- Key Options
- Output Files
- Known Motif Enrichment Only
- Scan for Specific Motifs
- Motif Comparison
- Create Custom Motif
- MEME Suite
- Extract Sequences from Peaks
- MEME (De Novo Discovery)
- MEME Options
conda install -c bioconda homer Configure genome (required once) perl /path/to/homer/configureHomer.pl -install hg38 perl /path/to/homer/configureHomer.pl -install mm10 Basic motif finding findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 With background regions findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 -bg background.bed Specify motif lengths to search findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 -len 8,10,12
What does the bio-chipseq-motif-analysis skill do?
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill motif-analysis-gptomics-bioskills-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.