R/ndex.R

#' The ndexr package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX objects. 
#'
#' \tabular{ll}{
#' Package: \tab ndexr\cr
#' Type: \tab Package\cr
#' Version: \tab 1.19.2\cr
#' Date: \tab 2016-12-02\cr
#' License: \tab BSD_3_clause\cr
#' }
#'
#' @author Florian Auer \email{florian.auer@informatik.uni-augsburg.de}
#' @author Zaynab Hammoud \email{zaynab.hammoud@informatik.uni-augsburg.de}
#' @author Frank Kramer \email{frank.kramer@informatik.uni-augsburg.de}
#' @name ndexr-package
#' @aliases ndexr
#' @docType package
#' @title NDEx R client library
#' @keywords package
#' @examples
#' \dontrun{
#' require(ndexr)
#' ## login to the NDEx server
#' ndexcon <- ndex_connect("username", "password")
#' 
#' ## search the networks for "EGFR"
#' networks <- ndex_find_networks(ndexcon, "EGFR")
#' head(networks, 3)
#' 
#' ## UUID of the first search result
#' networkId <- networks[1,'externalId']
#' networkId
#' 
#' ## get summary of the network
#' ndex_network_get_summary(ndexcon, networkId)
#' 
#' ## get the entire network as RCX object
#' rcx <- ndex_get_network(ndexcon, networkId)
#' 
#' ## show the content (aspects) of the network
#' rcx$metaData
#' 
#' ## visualize the network with RCX
#' RCX::visualize(rcx)
#' 
#' ## upload network as a new network to the NDEx server
#' networkId <- ndex_create_network(ndexcon, rcx)
#' 
#' ## do some other fancy stuff with the network, then
#' ## update the network on the server
#' networkId <- ndex_update_network(ndexcon, rcx)
#' 
#' ## realize, you did bad things to the poor network, so better 
#' ## delete it on the server
#' ndex_delete_network(ndexcon, networkId)
#' }
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frankkramer-lab/ndexr documentation built on April 4, 2023, 7:19 p.m.