Version Compatibility

Reference examples tested with: pySCENIC 0.12+, ctxcore 0.2+, arboreto 0.1.6+, scanpy 1.10+, loompy 3.0+.

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

The motif-DB machinery lives in ctxcore; a ctxcore/feather-format version mismatch is the most common silent failure. pySCENIC is most reliable on a dedicated Python 3.10 environment.

SCENIC Regulons

"Identify transcription factor regulons and score TF activity from my scRNA-seq data" -> Run the pySCENIC three-step pipeline: infer TF-target co-expression with GRNBoost2, prune to direct targets by cis-regulatory motif enrichment with cisTarget, then score per-cell regulon activity with AUCell.

• CLI: pyscenic grn -> pyscenic ctx -> pyscenic aucell
• Python: arboreto_with_multiprocessing.py for the GRN step (avoids the dask breakage)