## ---- 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)