Registration and Call for Abstracts Open for Bioc2024

synaptome.db

This is the development version of synaptome.db; for the stable release version, see synaptome.db.

Synamptosome Proteome Database


Bioconductor version: Development (3.19)

The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.

Author: Anatoly Sorokin [aut], Oksana Sorokina [aut, cre], J. Douglas Armstrong [aut]

Maintainer: Oksana Sorokina <oksana.sorokina at ed.ac.uk>

Citation (from within R, enter citation("synaptome.db")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("synaptome.db")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("synaptome.db")
synaptome_db_query HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version 0.99.16
License Artistic-2.0
Depends R (>= 3.5.0), synaptome.data
Imports DBI, RSQLite, dplyr, dbplyr, igraph, Rdpack, AnnotationHub, utils
System Requirements
URL
Bug Reports https://github.com/lptolik/synaptome.db/issues/
See More
Suggests rmarkdown, knitr, pander, testthat, devtools, markdown, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package synaptome.db_0.99.16.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/synaptome.db/
Package Downloads Report Download Stats