Version Compatibility

Reference examples tested with: Cicero 1.20+, monocle3 1.3+, ArchR 1.0.2+, SCENIC+ 1.0+, pycisTopic 1.0+, Signac 1.13+, GenomicRanges 1.54+, GenomicInteractions 1.36+, BSgenome.Hsapiens.UCSC.hg38 1.4+.

Verify before use:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• Python: pip show <package> then help(module.function) to check signatures

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

Co-accessibility (cis-Regulatory Linkage)

"Which enhancers connect to which promoters in my scATAC data?" -> Use cell-to-cell variability in joint accessibility of nearby peaks to infer cis-regulatory connections without explicit RNA expression. Output is a peak-pair graph with co-accessibility scores; thresholding produces enhancer-gene candidate pairs.

• R: cicero::run_cicero(input_cds, genomic_coords) -> peak-pair connection scores
• R: ArchR::addCoAccessibility(proj) -> ArchR-internal Cicero wrapper
• Python: pycisTopic + SCENIC+ for network-level inference combining ATAC + RNA + motifs

Co-accessibility is NOT 3D contact; it's a statistical association based on cell-to-cell co-variation. Strong co-accessibility correlates with Hi-C/Micro-C contacts (~30-50% concordance) but is not equivalent.