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synaptome.db

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

Synamptosome Proteome Database

Bioconductor version: Development (3.18)

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 "4.3") 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 0.99.12
License Artistic-2.0
Depends R (>= 3.5.0), synaptome.data
Imports DBI, RSQLite, dplyr, dbplyr, igraph, Rdpack, AnnotationHub, utils
Linking To
Suggests rmarkdown, knitr, pander, testthat, devtools, markdown
System Requirements
Enhances
URL
Bug Reports https://github.com/lptolik/synaptome.db/issues/
See More
Depends On Me
Imports Me BioNAR
Suggests Me
Links To Me

Package Archives

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

Source Package synaptome.db_0.99.12.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/synaptome.db/
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