synaptome.db

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see synaptome.db.

Synamptosome Proteome Database

Bioconductor version: 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")

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

Need some help? Ask on the Bioconductor Support site!

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/

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 (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url	https://bioconductor.org/packages/synaptome.db/
Package Downloads Report	Download Stats