## ----echo = FALSE-------------------------------------------------------------
knitr::opts_chunk$set(
  eval=FALSE
)

## -----------------------------------------------------------------------------
# if(!"RCy3" %in% installed.packages()){
#     install.packages("BiocManager")
#     BiocManager::install("RCy3")
# }
# library(RCy3)
# 
# if(!"ndexr" %in% installed.packages()){
#     install.packages("BiocManager")
#     BiocManager::install("ndexr")
# }
# library(ndexr)

## -----------------------------------------------------------------------------
# ndexcon <- ndex_connect()

## -----------------------------------------------------------------------------
# networks <- ndex_find_networks(ndexcon, "Breast Cancer")
# print(networks[,c("name","externalId","nodeCount","edgeCount")])

## -----------------------------------------------------------------------------
# networks <- ndex_find_networks(ndexcon, "BRCA")
# print(networks[,c("name","externalId","nodeCount","edgeCount")])

## -----------------------------------------------------------------------------
# networkId = networks$externalId[1]
# network = ndex_get_network(ndexcon, networkId)
# print(network)

## -----------------------------------------------------------------------------
# brca.net.suid <- importNetworkFromNDEx(networkId)

## -----------------------------------------------------------------------------
# ig2 <- makeSimpleIgraph()
# net.suid <- createNetworkFromIgraph(ig2, 'Simple Network', 'Simple Collection')

## -----------------------------------------------------------------------------
# user <- "your_NDEx_account_username"  #replace with your info
# pass <- "your_NDEx_account_password"  #replace with your info
# exportNetworkToNDEx(user, pass, isPublic=TRUE, network=net.suid)