Synaptome.db: a bioconductor package for synaptic proteomics data.

ABSTRACT

Summary: 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. Availability and implementation 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. Supplementary information Supplementary data are available at Bioinformatics Advances online.