synapser

The synapser package provides an interface to Synapse, a collaborative workspace for reproducible data intensive research projects, providing support for:

• integrated presentation of data, code and text
• fine grained access control
• provenance tracking

The synapser package lets you communicate with the Synapse platform to create collaborative data analysis projects and access data using the R programming language. Other Synapse clients exist for Python, Java, and the web browser.

Installation

synapser is available as a ready-built package for Microsoft Windows and Mac OSX. For Linux systems, it is available to install from source. Please also check out our System Dependencies article for instructions on how to install system dependencies on Linux environments.

synapser can be installed or upgraded using the standard install.packages() command, adding the Sage Bionetworks R Archive Network (RAN) to the repository list, e.g.:

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))

Alternatively, edit your ~/.Rprofile and configure your default repositories:

options(repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))

after which you may run install.packages without specifying the repositories:

install.packages("synapser")

If you have been asked to validate a release candidate, please use:

install.packages("synapser", repos=c("http://staging-ran.synapse.org", "http://cran.fhcrc.org"))

Note for Windows and Mac users

If you are running on Windows or Mac OSX and compiled R from source rather than installing it from a pre-built installer, by default R will attempt to install packages by compiling them from source as well rather than using the available ready-built packages. The toolchain necessary to build synapser includes some dependencies that may not be available even on a system that successfully compiled R and installation may fail as a result. In such an environment you can force R to use the available ready-built packages by explicitly specifying the type argument of install.packages, e.g.:

On Mac

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="mac.binary")

On Windows:

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="win.binary")

Usage

To get started, try logging into Synapse. If you don’t already have a Synapse account, register here:

library(synapser)
synLogin()

Please visit the synapser docs site or view our vignettes for using the synapser package:

browseVignettes(package="synapser")

Usage Examples:

knit2synapse

Knit RMarkdown files to Synapse wikis

syndccutils

Code for managing data coordinating operations (e.g., development of the CSBC/PS-ON Knowledge Portal and individual Center pages) for Sage-supported communities through Synapse.