Version Compatibility

Reference examples tested with: Signac 1.13+, Seurat 5.0+, ArchR 1.0+

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

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• Python (SnapATAC2 alternative): pip show snapatac2 then help(module.function)

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 fragments, QC on chromatin signal, reduce dimensions with TF-IDF/LSI, cluster, call consensus peaks per cell type, and score TF motif activity.

• R: Signac::CreateChromatinAssay() -> RunTFIDF() -> FindTopFeatures() -> RunSVD() -> RunChromVAR()
• R (large data, on-disk): ArchR::createArrowFiles() -> addIterativeLSI() -> addReproduciblePeakSet()
• Python (scverse, >1M cells): snapatac2.pp.add_tile_matrix() -> tl.spectral() -> tl.macs3()

Governing Principle