{"id":22777288,"url":"https://github.com/omicsdi/ddir","last_synced_at":"2025-04-15T12:26:51.400Z","repository":{"id":97524850,"uuid":"45335358","full_name":"OmicsDI/ddiR","owner":"OmicsDI","description":"An R package to access to Omics Discovery Index API","archived":false,"fork":false,"pushed_at":"2020-03-30T16:18:10.000Z","size":308467,"stargazers_count":2,"open_issues_count":0,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-28T20:06:57.021Z","etag":null,"topics":["multiomics","omicsdi","r","rest-client"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OmicsDI.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,"governance":null}},"created_at":"2015-11-01T09:55:46.000Z","updated_at":"2020-03-30T16:18:13.000Z","dependencies_parsed_at":"2023-05-01T05:54:44.583Z","dependency_job_id":null,"html_url":"https://github.com/OmicsDI/ddiR","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2FddiR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2FddiR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2FddiR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2FddiR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OmicsDI","download_url":"https://codeload.github.com/OmicsDI/ddiR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249070440,"owners_count":21207841,"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":["multiomics","omicsdi","r","rest-client"],"created_at":"2024-12-11T19:13:41.448Z","updated_at":"2025-04-15T12:26:51.356Z","avatar_url":"https://github.com/OmicsDI.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Travis build status](https://travis-ci.org/enriquea/ddiR.svg?branch=master)](https://travis-ci.org/enriquea/ddiR)\n\n[ddiR](https://github.com/BD2K-DDI/ddiR)\n======\n\nAn [R package](https://github.com/BD2K-DDI/ddiR) to obtain data from the Omics Discovery Index ([OmicsDI](http://www.omicsdi.org). It uses its RESTful Web Services at [OmicsDI WS](http://www.omicsdi.org/ws/) for that purpose.  \n\nCurrently, the following domain entities are supported:  \n\n* Dataset as S4 objects, including methods to get them from OmicsDI by accession and `as.data.frame`  \n* Publication as S4 objects, including methods to get them from OmicsDI by accession and `as.data.frame`  \n* Term as S4 objects, including methods to get them from OmicsDI by term and `as.data.frame`  \n\n### Installation  \n\nFirst, we need to install `devtools`:  \n\n    install.packages(\"devtools\")\n    library(devtools)\n   \nThen we just call  \n\n    install_github(\"enriquea/ddiR\")\n    library(ddiR)\n\n### Examples\n\n- This example retrives all dataset details given accession and database identifier\n\n```R\n\nlibrary(ddiR)\n\ndataset = get.DatasetDetail(accession=\"PXD000210\", database=\"pride\")\n\n# print dataset full name\nget.dataset.name(dataset)\n\n# print dataset omics type\nget.dataset.omics(dataset)\n\n```\n\n- Access to all datasets for NOTCH1 gene\n\n```R\n\ndatasets \u003c- search.DatasetsSummary(query = \"NOTCH1\")\n\nsink(\"outfile.txt\")\nfor(datasetCount in seq(from = 0, to = datasets@count, by = 100)){\n\n    datasets \u003c- search.DatasetsSummary(query = \"NOTCH1\", start = datasetCount, size = 100)\n\n    for(dataset in datasets@datasets){\n             dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))\n             print(paste(dataset.id(dataset), get.dataset.omics(dataset), get.dataset.link(dataset)))\n            }\n    }\n}\nsink()\n\n```\n\n- Getting the dataset IDs and full link of 20 Genomics studies in Cancer\n\n```R\n\ndatasets \u003c- search.DatasetsSummary(query = \"Cancer AND Genomics\")\n\nfor(dataset in datasets@datasets){\n    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))\n    print(paste(dataset.id(dataset), get.dataset.link(dataset), sep = ' '))\n}\n\n```\n\n- Print the dataset IDs and short description of 20 Proteomics studies for tumor supressor p53\n\n```R\n\ndatasets \u003c- search.DatasetsSummary(query = \"p53 AND Proteomics\")\n\nfor(dataset in datasets@datasets){\n    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))\n    print(paste(dataset.id(dataset), get.dataset.name(dataset), sep = ' '))\n}\n\n```\n\n- Getting Proteomics studies in Heart tissue from PRIDE database\n\n```R\n\ndatasets \u003c- search.DatasetsSummary(query = \"Heart\")\n\nfor(dataset in datasets@datasets){\n    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))\n    if(database(dataset)=='pride')\n    print(paste(dataset.id(dataset), get.dataset.tissues(dataset), get.dataset.omics(dataset), sep = ' '))\n}\n\n```\n\n- This exmaple shows how retrieve all the metadata similarity scores by using the R-package ddiR. \n\n```R\n\ndatasets \u003c- search.DatasetsSummary(query = \"*:*\")\ni  = 0\nsink(\"outfile.txt\")\nfor(datasetCount in seq(from = 0, to = datasets@count, by = 100)){\n\n    datasets \u003c- search.DatasetsSummary(query = \"*:*\", start = datasetCount, size = 100)\n\n    for(dataset in datasets@datasets){\n            Similar = get.MetadataSimilars(accession = dataset@dataset.id, database = dataset@database)\n            rank = 0\n            for(similarDataset in Similar@datasets){\n                print(paste(dataset@dataset.id, similarDataset@dataset.id, similarDataset@score, dataset@omics.type, rank))\n                rank = rank + 1\n            }\n    }\n}\nsink()\n\n```\n\n### Maintainers\n\n[Yasset Perez-Riverol](https://github.com/ypriverol)   \n[Ariana Barbera Betancourt](http://github.com/abb44)   \n[Enrique Audain](https://github.com/enriquea)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fddir","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fomicsdi%2Fddir","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fddir/lists"}