{"id":26448828,"url":"https://github.com/adeschen/enrichviewnet","last_synced_at":"2025-03-18T14:42:32.242Z","repository":{"id":80199698,"uuid":"351899814","full_name":"adeschen/enrichViewNet","owner":"adeschen","description":"From functional enrichment results to biological networks","archived":false,"fork":false,"pushed_at":"2024-04-11T02:01:55.000Z","size":15618,"stargazers_count":5,"open_issues_count":4,"forks_count":1,"subscribers_count":3,"default_branch":"devel","last_synced_at":"2024-04-12T07:23:11.203Z","etag":null,"topics":["cystocape","functional-enrichment","network","r-package"],"latest_commit_sha":null,"homepage":"https://adeschen.github.io/enrichViewNet/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/adeschen.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2021-03-26T20:08:22.000Z","updated_at":"2024-04-15T01:55:37.172Z","dependencies_parsed_at":"2024-02-09T22:28:05.637Z","dependency_job_id":"c8d52d9b-9a2f-48e6-ac67-fb949985e25f","html_url":"https://github.com/adeschen/enrichViewNet","commit_stats":null,"previous_names":["adeschen/gprofiler2cytoscape"],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FenrichViewNet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FenrichViewNet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FenrichViewNet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FenrichViewNet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/adeschen","download_url":"https://codeload.github.com/adeschen/enrichViewNet/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244243662,"owners_count":20422112,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cystocape","functional-enrichment","network","r-package"],"created_at":"2025-03-18T14:42:31.727Z","updated_at":"2025-03-18T14:42:32.236Z","avatar_url":"https://github.com/adeschen.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check-bioc](https://github.com/adeschen/enrichViewNet/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/adeschen/enrichViewNet/actions/workflows/check-bioc.yml)\n[![codecov](https://codecov.io/gh/adeschen/enrichViewNet/graph/badge.svg?token=N3RA2934V5)](https://codecov.io/gh/adeschen/enrichViewNet)\n[![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)\n\u003c!-- badges: end --\u003e\n\n\nThe **enrichViewNet** package enables the transformation of \nfunctional enrichment results, formatted as the results obtained  by [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html), \ninto networks. \n\nFirst, the **enrichViewNet** package enables the \nvisualization of enrichment results a [Cytoscape](https://cytoscape.org/) \nnetwork where significant terms \n(Gene Ontology/Reactome/Transcription Factor/etc..) and \ngenes are nodes. In this network, edges connect genes that are part of the\nenrichment request to their terms. \n\nIn addition, the **enrichViewNet** package also provides the option to \ncreate enrichment maps from functional enrichment results. \nEnrichment maps, as introduced in the Bioconductor \n[enrichplot](https://bioconductor.org/packages/release/bioc/html/enrichplot.html) package, \nenable the visualization of enriched terms \ninto a network with edges connecting overlapping genes. Thus, enriched terms \nwith overlapping genes cluster together.\n\n## Bioconductor Package ##\n\n[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/enrichViewNet.svg)](https://bioconductor.org/packages/enrichViewNet)\n\nThe **enrichViewNet** package is now an official package \nof [Bioconductor](http://bioconductor.org/). \n\nThe current Bioconductor release can be directly downloaded from their website:\n[Current release](https://bioconductor.org/packages/enrichViewNet/)\n\n\n## Authors ##\n\n[Astrid Desch\u0026ecirc;nes](http://ca.linkedin.com/in/astriddeschenes \"Astrid Desch\u0026ecirc;nes\"), \n[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau \"Pascal Belleau\"), \n[Robert L Faure](https://www.crchudequebec.ulaval.ca/en/research/researchers/robert-l-faure/), \n[Maria J Fernandes](https://www.crchudequebec.ulaval.ca/en/research/researchers/maria-fernandes/),\n[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/) and \n[David A Tuveson](https://tuvesonlab.labsites.cshl.edu/)\n\n## License ##\n\nThis package and the underlying **enrichViewNet** code are distributed under \nthe Artistic license 2.0. You are free to use and redistribute this software. \n\nFor more information on Artistic 2.0 License see\n[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)\n\n\n## Documentation ##\n\n[enrichViewNet Website](https://adeschen.github.io/enrichViewNet/)\n\n[enrichViewNet Get Started](https://adeschen.github.io/enrichViewNet/articles/enrichViewNet.html)\n\n\n## Installation ##\n\nTo install the latest version accessible, the \n[devtools](https://cran.r-project.org/web/packages/devtools/index.html) \npackage is required.\n\n     ## Load required package\n     library(devtools)\n\n     ## Install the latest version of enrichViewNet\n     devtools::install_github('adeschen/enrichViewNet')\n\n\nTo install this package \nfrom [Bioconductor](https://bioconductor.org), start R \n(version 4.3 or later) and enter: \n\n     if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n        install.packages(\"BiocManager\")\n\n     BiocManager::install(\"enrichViewNet\")\n\n\n## Bugs/Feature requests ##\n\nIf you have any bugs or feature requests, \n[let us know](https://github.com/adeschen/enrichViewNet/issues). \n\nThanks!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadeschen%2Fenrichviewnet","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadeschen%2Fenrichviewnet","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadeschen%2Fenrichviewnet/lists"}