{"id":20930672,"url":"https://github.com/intermine/interminer","last_synced_at":"2025-07-08T20:32:55.236Z","repository":{"id":43660362,"uuid":"47987362","full_name":"intermine/InterMineR","owner":"intermine","description":"R package for InterMine","archived":false,"fork":false,"pushed_at":"2022-04-05T14:19:21.000Z","size":8731,"stargazers_count":18,"open_issues_count":19,"forks_count":16,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-06-11T01:41:31.585Z","etag":null,"topics":["biology","genomics","intermine","r"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/intermine.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-12-14T16:34:44.000Z","updated_at":"2023-12-30T18:34:02.000Z","dependencies_parsed_at":"2022-09-24T00:51:17.678Z","dependency_job_id":null,"html_url":"https://github.com/intermine/InterMineR","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/intermine/InterMineR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2FInterMineR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2FInterMineR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2FInterMineR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2FInterMineR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/intermine","download_url":"https://codeload.github.com/intermine/InterMineR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2FInterMineR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264343839,"owners_count":23593796,"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":["biology","genomics","intermine","r"],"created_at":"2024-11-18T21:35:23.988Z","updated_at":"2025-07-08T20:32:55.210Z","avatar_url":"https://github.com/intermine.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"Master: [![Build Status: master][travis-badge-master]][ci] Dev: [![Build Status: dev][travis-badge-dev]][ci]\n\n# InterMine-R\n\n\u003cimg src=\"https://cdn.rawgit.com/Bioconductor/BiocStickers/e3a0fb08/InterMineR/InterMineR.png\" width=\"200\" /\u003e\n\nR package for accessing InterMine instances \n\n## Installation\n\nInterMineR has been added to [Bioconductor](https://bioconductor.org/packages/release/bioc/html/InterMineR.html).\n\nTo install this package, start R and enter:\n\n`## try http:// if https:// URLs are not supported`\n\n`if (!requireNamespace(\"BiocManager\", quietly=TRUE))`\n    `install.packages(\"BiocManager\")`\n\n`BiocManager::install(\"InterMineR\")`\n\nIn case installation for RCurl fails showing the error`installation of package ‘RCurl’ had non-zero exit status`, install libxml2-dev, libcurl4-openssl-dev and aptitude on you system using the following commands :\n \n `sudo apt-get install aptitude`\n\n `sudo apt-get install libcurl4-openssl-dev`\n\n `sudo apt-get install libxml2-dev`\n\n## Usage\n\nSee HTML vignettes for detailed API and tutorials:\n\n* vignettes/InterMineR.Rmd\n* vignettes/Enrichment_Analysis_and_Visualization.Rmd\n* vignettes/FlyMine_Genomic_Visualizations.Rmd\n\n## Contributing\n\n1. Fork it!\n2. Create your feature branch: `git checkout -b my-new-feature`\n3. Commit your changes: `git commit -am 'Add some feature'`\n4. Push to the branch: `git push origin my-new-feature`\n5. Submit a pull request :D\n\n## Credits\n\nBing Wang:\n\n* InterMineR package creation (first edition)\n* Established the first query system (queries as list objects)\n* Vignette creation (first edition)\n\nKonstantinos Kyritsis:\n\n* InterMineR package update to:\n  1. Operate with the [InterMine web services](http://intermine.readthedocs.io/en/latest/web-services/).\n  2. Comply with the standards of [Bioconductor submission](https://www.bioconductor.org/developers/package-submission/).\n  3. Retrieve the available Mines from the [InterMine registry](http://registry.intermine.org/).\n* Established the second query system (queries as `InterMineR-class` objects)\n* Addition of enrichment analysis functionality and convertion of the results to `GeneAnswer-class` objects\n* Addition of functionality for converting InterMineR-retrieved data to `GRanges-class` and `RangedSummarizedExperiment-class` objects\n* Additional functions:\n  1. `simplifyResult` function for flattened results display.\n  2. `listDatasets` and `getDatasets` to retrieve information about the available datasets in each Mine.\n* Vignette update (second edition)\n* Addition of tutorials for *Enrichment Analysis and Visualization* and *FlyMine Genomic Visualizations* with InterMineR\n\nCelia Sanchez Laorden\n\n* Created the listManager class for dealing with lists of objects within InterMineR\n* Created methods get_list, delete_listand create_list\n* Created functions  intersect, union, difference and subtract.\n* Created auxiliary methods: GET_api_list which returns the response object of the Request, get_unused_list_name which checks if the name given by the\nuser has been already used and, in such a case, provides a new one, and do_operation which creates a new list results of an operation. \n\n\n\n## License\n\nLGPL. See LICENSE for details.\n\n[travis-badge-master]: https://travis-ci.org/intermine/InterMineR.svg?branch=master\n[ci]: https://travis-ci.org/intermine/InterMineR\n[travis-badge-dev]: https://travis-ci.org/intermine/InterMineR.svg?branch=dev\n\n## Stickers\nSticker templates are available from [BiocStickers](https://github.com/Bioconductor/BiocStickers/tree/master/InterMineR) - or find us at a conference to pick some up in person. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Finterminer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fintermine%2Finterminer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Finterminer/lists"}