Package: ndexr 1.35.0

Florian Auer

ndexr: NDEx R client library

This 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 object and as igraph representation.

Authors:Florian Auer [cre, aut], Frank Kramer [ctb], Alex Ishkin [ctb], Dexter Pratt [ctb]

ndexr_1.35.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ndexr/json (API)

# Install 'ndexr' in R:

install.packages('ndexr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/frankkramer-lab/ndexr/issues

On BioConductor:ndexr-1.35.0(bioc 3.24)ndexr-1.34.0(bioc 3.23)

pathways dataimport network

6.56 score 9 stars 50 scripts 44 exports 33 dependencies

Last updated from:618bdcaf57. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	150
linux-devel-x86_64	ERROR	218
source / vignettes	OK	190
linux-release-x86_64	ERROR	181
macos-release-arm64	ERROR	115
macos-oldrel-arm64	ERROR	84
windows-devel	ERROR	109
windows-release	ERROR	111
windows-oldrel	ERROR	100
wasm-release	OK	157

Exports:ndex_config ndex_connect ndex_create_group ndex_create_network ndex_create_user ndex_delete_group ndex_delete_network ndex_delete_user ndex_find_groups ndex_find_networks ndex_find_user_byId ndex_find_user_byName ndex_find_users ndex_get_group ndex_get_network ndex_group_delete_membership ndex_group_list_networks ndex_group_list_users ndex_group_network_get_permission ndex_group_set_membership ndex_network_aspect_get_metadata ndex_network_delete_permission ndex_network_get_aspect ndex_network_get_metadata ndex_network_get_permission ndex_network_get_provenance ndex_network_get_summary ndex_network_set_systemProperties ndex_network_update_aspect ndex_network_update_permission ndex_network_update_profile ndex_update_group ndex_update_network ndex_update_user ndex_user_change_password ndex_user_forgot_password ndex_user_get_networksummary ndex_user_get_showcase ndex_user_list_groups ndex_user_list_permissions ndex_user_mail_password ndex_user_show_group ndex_user_show_permission ndex_verify_user

Dependencies:askpass cli cpp11 curl dplyr generics glue httr igraph jsonlite lattice lifecycle magrittr Matrix mime openssl pillar pkgconfig plyr purrr R6 Rcpp RCX rlang stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr

NDExR - R implementaion for NDEx server API

Rendered fromndexr-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-10-27
Started: 2017-04-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
NDEx R client library	ndexr-package ndexr
NDEx server api configuration	ndex_config
Connect to NDEx REST API	ndex_connect
Create Group	ndex_create_group
Create a Network at a server from RCX data	ndex_create_network
Create a user	ndex_create_user
Delete Group	ndex_delete_group
Delete a network	ndex_delete_network
Delete User	ndex_delete_user
Search groups in NDEx	ndex_find_groups
Search networks in NDEx (by description)	ndex_find_networks
Get User By UUID	ndex_find_user_byId
Get User By Name	ndex_find_user_byName
Search user in NDEx	ndex_find_users
Get a Group	ndex_get_group
Get complete network	ndex_get_network
Remove a Group Member	ndex_group_delete_membership
Get Network Permissions of a Group	ndex_group_list_networks
Get Members of a Group	ndex_group_list_users
Get Group Permission for a Specific Network	ndex_group_network_get_permission
Add or Update a Group Member	ndex_group_set_membership
Get the Metadata Associated with a Network UUID	ndex_network_aspect_get_metadata
Delete Network Permission	ndex_network_delete_permission
Get a Network Aspect As CX	ndex_network_get_aspect
Get Network CX Metadata Collection	ndex_network_get_metadata
Get All Permissions on a Network	ndex_network_get_permission
Get Network Provenance	ndex_network_get_provenance
Get NetworkSummary by Network UUID	ndex_network_get_summary
Set Network System Properties	ndex_network_set_systemProperties
Update an Aspect of a Network	ndex_network_update_aspect
Update Network Permission	ndex_network_update_permission
Update Network Profile	ndex_network_update_profile
Update Group	ndex_update_group
Update an Entire Network as CX	ndex_update_network
Update User	ndex_update_user
Change Password	ndex_user_change_password
Forgot Password	ndex_user_forgot_password
Get User's Account Page Networks	ndex_user_get_networksummary
Get User's Showcase Networks	ndex_user_get_showcase
Get User's Group Memberships	ndex_user_list_groups
Get User's Network Permissions	ndex_user_list_permissions
Email New Password	ndex_user_mail_password
Get User's Membership in Group	ndex_user_show_group
Get User's Permission for Network	ndex_user_show_permission
Verify a User	ndex_verify_user