gene-tidy

gene-tidy cleans messy tables of human gene and protein identifiers by mapping approved symbols, aliases, previous symbols, Ensembl gene, UniProt, Entrez, RefSeq and HGNC identifiers to current HGNC approved symbols with cross-references.

Key Features:

• Offline Operation: Works fully offline against a bundled static HGNC complete set snapshot.
• Identifier Mapping: Maps approved symbols, aliases, previous symbols, Ensembl gene, UniProt, Entrez, RefSeq and HGNC identifiers to current HGNC approved symbols with cross-references.
• Excel Date Corruption Recovery: Recovers Excel date-corrupted gene symbols where the original is unambiguous and flags them for manual review otherwise.
• No Row Dropping: Never drops an input row; one-to-many and uncertain mappings are flagged for manual review rather than guessed silently.
• Audit Trail: Each run records the gene-tidy version and the exact HGNC release used, and writes a per-row audit table.
• Methods Paragraph Generation: Emits a paste-ready methods paragraph documenting the run.

Scientific Applications:

• Gene Identifier Standardization: Cleans messy gene/protein identifier tables in TXT, CSV, TSV and XLSX formats for downstream analysis.
• Cross-reference Generation: Produces current HGNC approved symbols with Ensembl, UniProt, Entrez and RefSeq cross-references for integrated omics analyses.

Methodology:

gene-tidy uses a bundled static HGNC complete set snapshot to map input identifiers to current HGNC approved symbols.