Version Compatibility

Reference examples tested with: biomaRt 2.58+, AnnotationDbi 1.66+, org.Hs.eg.db 3.18+, org.Mm.eg.db 3.18+, GenomicFeatures 1.54+, mygene 1.38+ (Python), pyensembl 2.3+, pandas 2.2+, rtracklayer 1.62+

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

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

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

Gene ID Mapping

"Convert gene IDs from X to Y" -> Query the appropriate annotation source (local org.db for speed, biomaRt for Ensembl-specific attributes, mygene for cross-database aliases, Ensembl REST for low-level access), with version pinning for reproducibility and explicit handling of one-to-many mappings, withdrawn symbols, and species-specific naming.

The Single Most Important Modern Insight -- Excel autocorrect renamed real genes

Ziemann, Eren, El-Osta 2016 Genome Biol 17:177 scanned 18 leading genomics journals and found ~20% of papers with Excel-attached supplementary gene lists had silently mangled symbols (SEPT2 -> 2-Sep, MARCH1 -> 1-Mar, ...). Five years later the problem persisted. HGNC's response (Bruford, Braschi, Denny, Jones, Seal, Tweedie 2020 Nat Genet 52:754) was to rename the affected genes: