homer-motif-analysis
Analyzes TF motif enrichment in ChIP-seq/ATAC-seq peaks using HOMER, enabling motif discovery and peak annotation for genomic studies.
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The homer-motif-analysis skill was audited on May 24, 2026 and we found 11 security issues across 3 threat categories. Review the findings below before installing.
Categories Tested
Security Issues
medium line 439
Template literal with variable interpolation in command context
SourceSKILL.md
| 439 | ```bash |
medium line 415
Python subprocess execution
SourceSKILL.md
| 415 | result = subprocess.run(cmd, capture_output=True, text=True) |
low line 92
Access to hidden dotfiles in home directory
SourceSKILL.md
| 92 | ls ~/.homer/data/genomes/hg38/ |
low line 96
Access to hidden dotfiles in home directory
SourceSKILL.md
| 96 | ls ~/.homer/data/knownTFs/ |
low line 124
Access to hidden dotfiles in home directory
SourceSKILL.md
| 124 | -g ~/.homer/data/genomes/hg38/chrom.sizes \ |
medium line 567
Access to hidden dotfiles in home directory
SourceSKILL.md
| 567 | | `ERROR: Genome not found` | Genome not installed via `installGenome.pl` | Run `installGenome.pl hg38`; confirm `~/.homer/data/genomes/hg38/` exists | |
medium line 568
Access to hidden dotfiles in home directory
SourceSKILL.md
| 568 | | `command not found: findMotifsGenome.pl` | HOMER binaries not in `$PATH` | Add HOMER bin directory to PATH: `export PATH=~/.homer/bin:$PATH` (or activate conda env) | |
medium line 572
Access to hidden dotfiles in home directory
SourceSKILL.md
| 572 | | `annotatePeaks.pl` gives all "Intergenic" | Genome annotation not installed | HOMER annotation requires `installGenome.pl` which downloads GTF; check `~/.homer/data/genomes/hg38/` contains `*.ann` f |
low line 578
External URL reference
SourceSKILL.md
| 578 | - [HOMER official documentation](http://homer.ucsd.edu/homer/) — comprehensive guide to all HOMER commands, parameters, and output formats |
low line 579
External URL reference
SourceSKILL.md
| 579 | - Heinz S et al. (2010) "Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities." *Molecular Cell* 38(4):576–589. |
low line 581
External URL reference
SourceSKILL.md
| 581 | - [JASPAR 2024 database](https://jaspar.elixir.no/) — curated TF binding motif database used by HOMER for known motif enrichment |
Scanned on May 24, 2026
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Categoryeducation research
UpdatedJune 15, 2026
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