Version Compatibility

Reference examples tested with: BioPython 1.83+, bedtools 2.31+, matplotlib 3.8+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Motif Analysis

"Find enriched motifs in my ChIP-seq peaks" → Discover de novo DNA-binding motifs and test for known TF motif enrichment in peak sequences.

• CLI: findMotifsGenome.pl peaks.bed hg38 output/ (HOMER), meme-chip -db JASPAR peaks.fa (MEME)

Identify DNA sequence motifs enriched in ChIP-seq or ATAC-seq peaks to discover transcription factor binding sites.

Tool Comparison