Version Compatibility

Reference examples tested with: DiffBind 3.12+, DESeq2 1.42+, edgeR 4.0+, csaw 1.36+, limma 3.58+, GenomicRanges 1.54+, ChIPseeker 1.38+, Subread 2.0+ (featureCounts), sva 3.50+, RUVSeq 1.36+.

Before using code patterns, verify installed versions match:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws unexpected errors, introspect the installed package and adapt rather than retrying.

Differential Accessibility

"Find chromatin regions that change accessibility between my conditions" -> Build a sample-by-region count matrix, normalize for library size and chromatin compaction, fit a generalized linear model (negative-binomial), and extract regions with significant accessibility change.

• R (consensus-peak workflow): DiffBind -> count -> normalize -> contrast -> analyze
• R (window-based, no peak set): csaw::windowCounts + filterWindowsGlobal + edgeR QL F-test
• R (existing peak-count matrix): DESeq2 or edgeR directly on featureCounts output

DiffBind is a wrapper around DESeq2 / edgeR with ATAC-aware defaults. csaw is the only peak-free option; it tests fixed-width sliding windows. The choice depends on whether peaks are stable across conditions (use DiffBind) or whether some condition has dramatically different peak structure (use csaw or rebuild consensus peaks).