biostudies-literatureUnknown2(1)Sorokina O<h4>Summary</h4>The neuronal synapse is underpinned by a large and diverse proteome but the molecular evidence is spread across many primary datasets. These data were recently curated into a single dataset describing a landscape of ∼8000 proteins found in studies of mammalian synapses. Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. Synaptome.db allows users to obtain the respective gene information, e.g. subcellular localization, brain region, gene ontology, disease association and construct custom protein-protein interaction network models for gene sets and entire subcellular compartments.<h4>Availability and implementation</h4>The package Synaptome.db is part of Bioconductor since release 3.14, https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html, it is open source and available under the Artistic license 2.0. The development version is maintained on GitHub (https://github.com/lptolik/synaptome.db). Full documentation including examples is provided in the form of vignettes on the package webpage.<h4>Supplementary information</h4>Supplementary data are available at <i>Bioinformatics Advances</i> online.Bioinformatics advancesvbac086https://www.ebi.ac.uk/biostudies/studies/S-EPMC9710567biostudies-literatureSynaptome.db: a bioconductor package for synaptic proteomics data.PMC9710567Armstrong JDSorokina OSorokin AfalseSynaptome.db: a bioconductor package for synaptic proteomics data.<h4>Summary</h4>The neuronal synapse is underpinned by a large and diverse proteome but the molecular evidence is spread across many primary datasets. These data were recently curated into a single dataset describing a landscape of ∼8000 proteins found in studies of mammalian synapses. Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. Synaptome.db allows users to obtain the respective gene information, e.g. subcellular localization, brain region, gene ontology, disease association and construct custom protein-protein interaction network models for gene sets and entire subcellular compartments.<h4>Availability and implementation</h4>The package Synaptome.db is part of Bioconductor since release 3.14, https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html, it is open source and available under the Artistic license 2.0. The development version is maintained on GitHub (https://github.com/lptolik/synaptome.db). Full documentation including examples is provided in the form of vignettes on the package webpage.<h4>Supplementary information</h4>Supplementary data are available at <i>Bioinformatics Advances</i> online.2022-01-01T00:00:00Z20222025-04-21T23:14:24.026Z2025-04-05T19:05:18.888ZS-EPMC97105673669934610.1093/bioadv/vbac086