Version Compatibility

Reference examples tested with: bedtools 2.31+, 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
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• 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.

Binding Site Annotation

"Annotate where my RBP binds in transcripts" → Map CLIP-seq peaks to genomic features (3'UTR, 5'UTR, CDS, introns, ncRNAs) to characterize RNA-binding protein target regions.

• R: ChIPseeker::annotatePeak() with transcript annotation databases
• CLI: bedtools intersect with gene model BED files

Using ChIPseeker (R)