Version Compatibility

Reference examples tested with: MACS2 2.2+, scanpy 1.10+

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

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

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

scATAC-seq Analysis

"Analyze my single-cell ATAC-seq data" → Process peak-barcode matrices, perform QC/filtering, reduce dimensions with LSI, cluster cells, call peaks per cluster, and score motif activity.

• R: Signac::CreateChromatinAssay() → RunTFIDF() → FindTopFeatures() → RunSVD()
• R: ArchR::createArrowFiles() for large datasets

Analyze single-cell chromatin accessibility data to identify cell types and regulatory elements.

Tool Comparison