geneslator

geneslator is a comprehensive R package for gene identifier conversion and genome annotation across multiple model organisms. The package integrates data from several cross-organism databases and organism-specific resources within a single, coherent framework.

Key Features

• Multiple database integration: Integrates data from cross-organism databases (NCBI, Ensembl, UniProt, Alliance of Genome Resources, GO, KEGG, Reactome, Wikipathways) and organism-specific resources (HGNC, MGI, RGD, SGD, WormBase, Flybase, ZFIN, TAIR)
• Archive search: Supports searching using both current and archived gene identifiers in NCBI and Ensembl databases
• Alias resolution: Supports automatic disambiguation between symbols and aliases in annotations involving gene symbols
• Automatic download: Annotation databases are automatically downloaded when needed and cached locally
• Version management: Independent versioning system for databases with automatic update checks

Supported Organisms

• Human (Homo sapiens)
• Mouse (Mus musculus)
• Rat (Rattus norvegicus)
• Yeast (Saccharomyces cerevisiae)
• Worm (Caenorhabditis elegans)
• Fly (Drosophila melanogaster)
• Zebrafish (Danio rerio)
• Arabidopsis (Arabidopsis thaliana)

Installation

if (!requireNamespace("devtools", quietly = TRUE)) {
    install.packages("devtools")
}
devtools::install_github("knowmics-lab/geneslator", build_vignettes = TRUE)

Usage examples

library(geneslator)

# Check available organisms
availableOrganisms()

# Import human annotation database (download database automatically if needed)
human.db <- GeneslatorDb("Human")

# List all columns present in human annotation database 
columns(human.db)

# List all identifier columns present in human annotation database 
keytypes(gdb)

# Get gene symbols, full names and NCBI Gene IDs from Ensembl IDs using select()
select(human.db, keys = c("ENSG00000141510", "ENSG00000012048", "ENSG00000139618"),
       columns = c("SYMBOL", "GENENAME", "ENTREZID"), keytype = "ENSEMBL")

# Convert Ensembl IDs to gene symbols using mapIds()
mapIds(gdb, keys = c("ENSG00000139618", "ENSG00000141510"), column = "SYMBOL",
       keytype = "ENSEMBL")

# Get mouse orthologs for human genes
select(human.db, keys = c("TP53", "BRCA1", "EGFR"), columns = c("ORTHOMOUSE"),
       keytype = "SYMBOL")

# Get GO annotations for a set of genes
select(human.db, keys = c("7157", "672"), columns = c("SYMBOL", "GO", "GONAME"),
       keytype = "ENTREZID")

# Get KEGG pathways for a set of genes
select(human.db, keys = c("TP53", "BRCA1"), columns = c("KEGGPATH", "KEGGPATHNAME"),
       keytype = "SYMBOL")

Database Management

Annotation databases are automatically downloaded from when needed and cached locally.

When you import an annotation database in geneslator:

• If the database is not present in the local cache, it is automatically downloaded
• If the database is present but a newer version is available, you will be asked if you want to update it
• Files are saved in the R cache directory (visible with tools::R_user_dir("geneslator", "cache"))

# Import human database for the first time: the database is downloaded and saved in cache
gdb <- GeneslatorDb("Human")

# Import human database again: use file saved in local cache
gdb <- GeneslatorDb("Human")

Documentation

# Package vignette:
vignette("geneslator", package = "geneslator")

# Documentation:
help(package = "geneslator")

Citation

If you use geneslator in your work, please cite:

citation("geneslator")

Micale G, Cavallaro G, Privitera GF (2026). geneslator: A Comprehensive Gene Identifier Conversion Tool. R package version 0.99.0. https://github.com/knowmics-lab/geneslator

License

This package is released under the Artistic-2.0 license. See the LICENSE file for details.

Authors

• Giovanni Micale - Author and maintainer - ORCID
• Giulia Cavallaro - Author - ORCID
• Grete Francesca Privitera - Author - ORCID

University of Catania

Support

• Issues: https://github.com/knowmics-lab/geneslator/issues
• Email: giovanni.micale@unict.it

References

• NCBI Gene: https://www.ncbi.nlm.nih.gov/gene
• Ensembl: https://www.ensembl.org
• UniProt: https://www.uniprot.org
• Gene Ontology: http://geneontology.org
• KEGG: https://www.kegg.jp
• Reactome: https://reactome.org
• WikiPathways: https://www.wikipathways.org
• Alliance of Genome Resources: https://www.alliancegenome.org
• AnnotationDbi: Pages H, Carlson M, Falcon S, Li N (2024). AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor.