{"id":22731081,"url":"https://github.com/genentech/conmedclassify","last_synced_at":"2026-07-06T20:31:15.820Z","repository":{"id":66964192,"uuid":"478699617","full_name":"Genentech/ConMedClassify","owner":"Genentech","description":"Process clinical ADaM-format data and classify subjects into profiles based on their concomitant medication usage within a clinical trial.","archived":false,"fork":false,"pushed_at":"2022-04-14T05:25:15.000Z","size":29,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-07-21T16:46:07.747Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.png","metadata":{"files":{"readme":"README.Rmd","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-04-06T19:29:29.000Z","updated_at":"2023-04-28T15:30:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"5d64e830-a117-42f9-b0f4-7e97e8195991","html_url":"https://github.com/Genentech/ConMedClassify","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Genentech/ConMedClassify","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FConMedClassify","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FConMedClassify/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FConMedClassify/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FConMedClassify/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/ConMedClassify/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FConMedClassify/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281059632,"owners_count":26437057,"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","status":"online","status_checked_at":"2025-10-26T02:00:06.575Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-12-10T19:19:22.282Z","updated_at":"2025-10-26T04:49:48.410Z","avatar_url":"https://github.com/Genentech.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# ConMedClassify\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThis package stores sufficient demonstration data to perform a classification.\n\n```{r}\nlibrary(ConMedClassify)\n\n# load demo drug basket information\ndata(drug_baskets)\ndrug_baskets\n\n# load demo clinical data\ndata(demo_clinical_data)\ndplyr::glimpse(demo_clinical_data)\n\nas.data.frame(unnest_domain(demo_clinical_data[, c(\"STUDYID\", \"USUBJID\", \"nested.CM\")], nested.CM))\n\nas.data.frame(unnest_domain(demo_clinical_data[, c(\"STUDYID\", \"USUBJID\", \"nested.EX\")], nested.EX))\n\nas.data.frame(unnest_domain(demo_clinical_data[, c(\"STUDYID\", \"USUBJID\", \"nested.TTE\")], nested.TTE))\n```\n\nPerforming the classification results in a file of profiles\n\n```{r, eval = FALSE}\n# profile subjects into conmed profiles\nextract_conmed_profiles_to_tsv(demo_clinical_data, drug_baskets = drug_baskets, drug_basket_data_objects = NULL, treatments = \"trt1\")\n```\n\n```{r}\nres \u003c- readr::read_tsv(\"inst/outputs/ConMedProfiles_trial1_basket_demo.tsv\", col_types = \"c\")\ndplyr::glimpse(res)\n```\n\nWhen many of these are constructed they can be aggregated together into a single file per drug basket\n\n```{r, eval = FALSE}\n# merge all individual TSV files across studies into a single one for a given drug basket\naggregate_conmed_profile_tsv(input_tsv_path = \"outputs/\",\n                             tsv_pattern = '_basket_demo\\\\.tsv',\n                             basket_name = \"DEMO\",\n                             output_filename_prefix = \"outputs/CITDataMart_ConMedProfiles_\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fconmedclassify","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fconmedclassify","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fconmedclassify/lists"}