{ "_id": "6ae709c61e2c7b3a4f52fb55", "Package": "ndexr", "Type": "Package", "Title": "NDEx R client library", "Version": "1.35.0", "Date": "2018-04-27", "Authors@R": "c(\nperson(given = \"Florian\", family = \"Auer\",\nrole = c(\"cre\",\"aut\"),\nemail = \"florian.auer@informatik.uni-augsburg.de\",\ncomment = c(ORCID = \"0000-0002-5320-8900\")),\nperson(given = \"Frank\", family = \"Kramer\",\nrole = c(\"ctb\"),\nemail = \"frank.kramer@informatik.uni-augsburg.de\"),\nperson(given = \"Alex\", family = \"Ishkin\",\nrole = c(\"ctb\"),\nemail = \"aleksandr.ishkin@thomsonreuters.com\"),\nperson(given = \"Dexter\", family = \"Pratt\",\nrole = c(\"ctb\"),\nemail = \"depratt@ucsc.edu\"))", "Description": "This package offers an interface to NDEx servers, e.g. the\npublic server at http://ndexbio.org/. It can retrieve and save\nnetworks via the API. Networks are offered as RCX object and as\nigraph representation.", "License": "BSD_3_clause + file LICENSE", "RoxygenNote": "7.2.3", "Encoding": "UTF-8", "biocViews": "Pathways, DataImport, Network", "VignetteBuilder": "knitr", "URL": "https://github.com/frankkramer-lab/ndexr", "BugReports": "https://github.com/frankkramer-lab/ndexr/issues", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:44 UTC", "RemoteUrl": "https://github.com/bioc/ndexr", "RemoteRef": "HEAD", "RemoteSha": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 09:38:55 UTC", "User": "root" }, "Author": "Florian Auer [cre, aut] (ORCID:\n),\nFrank Kramer [ctb],\nAlex Ishkin [ctb],\nDexter Pratt [ctb]", "Maintainer": "Florian Auer ", "_user": "bioc", "_type": "src", "_file": "ndexr_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/f48e766ede729b4966fd2054c8eedf438aa14a0c0f11bf5518f94adf5a35dccb", "_filesize": 969988, "_sha256": "f48e766ede729b4966fd2054c8eedf438aa14a0c0f11bf5518f94adf5a35dccb", "_expires": "2027-02-09T09:43:32.000Z", "_created": "2026-11-01T09:38:55.000Z", "_published": "2026-11-01T09:43:34.438Z", "_upstream": "https://github.com/bioc/ndexr", "_status": "success", "_maintainer": { "name": "Florian Auer", "email": "florian.auer@informatik.uni-augsburg.de", "login": "florian-j-auer", "description": "", "uuid": 20659040, "orcid": "0000-0002-5320-8900" }, "_jobs": [ { "job": 124811088662, "time": 130, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13078392924" }, { "job": 124811088665, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13078147317" }, { "job": 124811088659, "time": 240, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13079105539" }, { "job": 124811088640, "time": 117, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13078702382" }, { "job": 124811088734, "time": 122, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13078767323" }, { "job": 124810316828, "time": 220, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "13078607238" }, { "job": 124811088681, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13078436722" }, { "job": 124811088673, "time": 101, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13078667572" }, { "job": 124811088709, "time": 102, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13079105246" }, { "job": 124811088817, "time": 111, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13078736370" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130", "_commit": { "id": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380344 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "RCX", "role": "Depends" }, { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "pathways", "dataimport", "network" ], "_stars": 9, "_contributors": [ { "user": "florian-j-auer", "count": 51, "uuid": 20659040 }, { "user": "donshikin", "count": 21, "uuid": 174282 }, { "user": "frankkramer", "count": 14, "uuid": 1914156 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "dexterpratt", "count": 8, "uuid": 1108652 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 466, "source": "https://www.bioconductor.org/packages/stats/bioc/ndexr" }, "_devurl": "https://github.com/frankkramer-lab/ndexr", "_searchresults": 56, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/ndexr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/frankkramer-lab/ndexr", "_realowner": "bioc", "_cranurl": false, "_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" ], "_help": [ { "page": "ndexr-package", "title": "NDEx R client library", "topics": [ "ndexr-package", "ndexr" ] }, { "page": "ndex_config", "title": "NDEx server api configuration", "topics": [ "ndex_config" ] }, { "page": "ndex_connect", "title": "Connect to NDEx REST API", "topics": [ "ndex_connect" ] }, { "page": "ndex_create_group", "title": "Create Group", "topics": [ "ndex_create_group" ] }, { "page": "ndex_create_network", "title": "Create a Network at a server from RCX data", "topics": [ "ndex_create_network" ] }, { "page": "ndex_create_user", "title": "Create a user", "topics": [ "ndex_create_user" ] }, { "page": "ndex_delete_group", "title": "Delete Group", "topics": [ "ndex_delete_group" ] }, { "page": "ndex_delete_network", "title": "Delete a network", "topics": [ "ndex_delete_network" ] }, { "page": "ndex_delete_user", "title": "Delete User", "topics": [ "ndex_delete_user" ] }, { "page": "ndex_find_groups", "title": "Search groups in NDEx", "topics": [ "ndex_find_groups" ] }, { "page": "ndex_find_networks", "title": "Search networks in NDEx (by description)", "topics": [ "ndex_find_networks" ] }, { "page": "ndex_find_user_byId", "title": "Get User By UUID", "topics": [ "ndex_find_user_byId" ] }, { "page": "ndex_find_user_byName", "title": "Get User By Name", "topics": [ "ndex_find_user_byName" ] }, { "page": "ndex_find_users", "title": "Search user in NDEx", "topics": [ "ndex_find_users" ] }, { "page": "ndex_get_group", "title": "Get a Group", "topics": [ "ndex_get_group" ] }, { "page": "ndex_get_network", "title": "Get complete network", "topics": [ "ndex_get_network" ] }, { "page": "ndex_group_delete_membership", "title": "Remove a Group Member", "topics": [ "ndex_group_delete_membership" ] }, { "page": "ndex_group_list_networks", "title": "Get Network Permissions of a Group", "topics": [ "ndex_group_list_networks" ] }, { "page": "ndex_group_list_users", "title": "Get Members of a Group", "topics": [ "ndex_group_list_users" ] }, { "page": "ndex_group_network_get_permission", "title": "Get Group Permission for a Specific Network", "topics": [ "ndex_group_network_get_permission" ] }, { "page": "ndex_group_set_membership", "title": "Add or Update a Group Member", "topics": [ "ndex_group_set_membership" ] }, { "page": "ndex_network_aspect_get_metadata", "title": "Get the Metadata Associated with a Network UUID", "topics": [ "ndex_network_aspect_get_metadata" ] }, { "page": "ndex_network_delete_permission", "title": "Delete Network Permission", "topics": [ "ndex_network_delete_permission" ] }, { "page": "ndex_network_get_aspect", "title": "Get a Network Aspect As CX", "topics": [ "ndex_network_get_aspect" ] }, { "page": "ndex_network_get_metadata", "title": "Get Network CX Metadata Collection", "topics": [ "ndex_network_get_metadata" ] }, { "page": "ndex_network_get_permission", "title": "Get All Permissions on a Network", "topics": [ "ndex_network_get_permission" ] }, { "page": "ndex_network_get_provenance", "title": "Get Network Provenance", "topics": [ "ndex_network_get_provenance" ] }, { "page": "ndex_network_get_summary", "title": "Get NetworkSummary by Network UUID", "topics": [ "ndex_network_get_summary" ] }, { "page": "ndex_network_set_systemProperties", "title": "Set Network System Properties", "topics": [ "ndex_network_set_systemProperties" ] }, { "page": "ndex_network_update_aspect", "title": "Update an Aspect of a Network", "topics": [ "ndex_network_update_aspect" ] }, { "page": "ndex_network_update_permission", "title": "Update Network Permission", "topics": [ "ndex_network_update_permission" ] }, { "page": "ndex_network_update_profile", "title": "Update Network Profile", "topics": [ "ndex_network_update_profile" ] }, { "page": "ndex_update_group", "title": "Update Group", "topics": [ "ndex_update_group" ] }, { "page": "ndex_update_network", "title": "Update an Entire Network as CX", "topics": [ "ndex_update_network" ] }, { "page": "ndex_update_user", "title": "Update User", "topics": [ "ndex_update_user" ] }, { "page": "ndex_user_change_password", "title": "Change Password", "topics": [ "ndex_user_change_password" ] }, { "page": "ndex_user_forgot_password", "title": "Forgot Password", "topics": [ "ndex_user_forgot_password" ] }, { "page": "ndex_user_get_networksummary", "title": "Get User's Account Page Networks", "topics": [ "ndex_user_get_networksummary" ] }, { "page": "ndex_user_get_showcase", "title": "Get User's Showcase Networks", "topics": [ "ndex_user_get_showcase" ] }, { "page": "ndex_user_list_groups", "title": "Get User's Group Memberships", "topics": [ "ndex_user_list_groups" ] }, { "page": "ndex_user_list_permissions", "title": "Get User's Network Permissions", "topics": [ "ndex_user_list_permissions" ] }, { "page": "ndex_user_mail_password", "title": "Email New Password", "topics": [ "ndex_user_mail_password" ] }, { "page": "ndex_user_show_group", "title": "Get User's Membership in Group", "topics": [ "ndex_user_show_group" ] }, { "page": "ndex_user_show_permission", "title": "Get User's Permission for Network", "topics": [ "ndex_user_show_permission" ] }, { "page": "ndex_verify_user", "title": "Verify a User", "topics": [ "ndex_verify_user" ] } ], "_readme": "https://github.com/bioc/ndexr/raw/HEAD/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "ndexr-vignette.Rmd", "filename": "ndexr-vignette.html", "title": "NDExR - R implementaion for NDEx server API", "author": "Florian J. Auer, Zaynab Hammoud, Frank Kramer", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Installation from Bioconductor", "Installation from GitHub", "Quick Start", "Connect to a server", "Find Networks", "Simple network operations", "RCX", "Example Workflow", "Aspects and Metadata", "NDEx Network properties", "API Compatibility with NDEx versions", "Server REST API configuration" ], "created": "2017-04-03 09:36:13", "modified": "2022-10-27 14:48:01", "commits": 11 } ], "_score": 6.605520523437469, "_indexed": true, "_nocasepkg": "ndexr", "_universes": [ "bioc", "florian-j-auer", "frankkramer-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-11-01T09:41:42.000Z", "distro": "resolute", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/fd7bdff16e3dfa537b8a2554f22705426b52b3241fde2f988266601e2079622c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.6.2", "os": "linux", "version": "1.35.0", "date": "2026-11-01T09:42:48.000Z", "distro": "resolute", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/6bbff374bd0036f3452f05129e606afe31f361e64897cc64f3ca86a4da11dfbb", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-11-01T09:40:50.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/dbdff7e2ea1a4d74c97d6a9a5bacb24689bf1eb5f8aa021048a8a4bf9140911c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.6.2", "os": "mac", "version": "1.35.0", "date": "2026-11-01T09:40:42.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/e4cdde933b3d66f3088a51c44a44e2f6c6ea6631ff9d3a684e2d9ec9534eca01", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-11-01T09:40:59.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/8dcdb7cac32638867d41295a1ca784bab35fe5067603e0d1ab61dc2b7bcd2a3b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-11-01T09:40:10.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/366b38e9b7d45506340159a57fbc108b356d65bb735204de2a03ca56371413da", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-11-01T09:40:22.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/7fa3d28e137ba85c27f5b4f31e8a8f72dc420ca31a0d1a19f85226368be688ef", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" }, { "r": "4.6.2", "os": "win", "version": "1.35.0", "date": "2026-11-01T09:40:16.000Z", "commit": "618bdcaf57100b76d66c33785d47d0d392f9f3ca", "fileid": "https://r2.ropensci.org/ead4494719acf72afb533b227cf6026239434de60123fe433c276788598ea1c9", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41293778130" } ] }