Version Compatibility

Reference examples tested with: GenomicRanges 1.54+, bedtools 2.31+, ggplot2 3.5+, samtools 1.19+

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

• 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.

Super-Enhancer Calling

"Identify super-enhancers from H3K27ac ChIP-seq" → Stitch nearby enhancer peaks and rank by signal to find large regulatory domains controlling cell identity genes.

• CLI: ROSE_main.py -g hg38 -i peaks.gff -r chip.bam -c input.bam

Identify super-enhancers (SEs) - large clusters of enhancers that control cell identity genes.

Background