{"id":25167167,"url":"https://github.com/biocomputingup/cagi-p16-assessment","last_synced_at":"2025-10-15T12:33:40.858Z","repository":{"id":81784648,"uuid":"87537312","full_name":"BioComputingUP/CAGI-p16-assessment","owner":"BioComputingUP","description":"https://genomeinterpretation.org/content/predict-how-variants-p16-tumor-suppressor-protein-affect-cell-proliferation","archived":false,"fork":false,"pushed_at":"2017-04-14T10:25:04.000Z","size":26,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-07-13T06:41:16.201Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/BioComputingUP.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,"publiccode":null,"codemeta":null}},"created_at":"2017-04-07T11:05:30.000Z","updated_at":"2017-04-07T11:31:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"91f66f7c-27d8-4436-ab7f-4582dbe6f170","html_url":"https://github.com/BioComputingUP/CAGI-p16-assessment","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BioComputingUP/CAGI-p16-assessment","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCAGI-p16-assessment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCAGI-p16-assessment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCAGI-p16-assessment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCAGI-p16-assessment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioComputingUP","download_url":"https://codeload.github.com/BioComputingUP/CAGI-p16-assessment/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCAGI-p16-assessment/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270899433,"owners_count":24664712,"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":"2025-08-17T02:00:09.016Z","response_time":129,"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":"2025-02-09T06:19:47.564Z","updated_at":"2025-10-15T12:33:35.835Z","avatar_url":"https://github.com/BioComputingUP.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CAGI-p16-assessment\n\n## Overview\n\nThis repository contains all the R scrips used for the assessment of the CAGI-3 [\"p16 challenge\"](https://genomeinterpretation.org/content/predict-how-variants-p16-tumor-suppressor-protein-affect-cell-proliferation).\n\nAll the scripts can be reused for performance assessment of bioinformatics tools to predict phenotypic effects of genetic variants of unknown significance (VUS).\n\n## Dependencies\nThe analysis requires the following R packages to be installed\n\n* [ROCR](https://cran.r-project.org/web/packages/ROCR/index.html)\n* [plotrix](https://cran.r-project.org/web/packages/plotrix/index.html)\n\n## Usage\n\nEach script can be run from a terminal as the example below\n\n``` \n  Rscript 1_main_numerical_assessment.R \n```\n\n## Details\n\nIn this section a brief description of each script is given\n\nScript | Description\n------------ | -------------\n1 | calculates the main numerical measures (i.e. correlations, AUC, RMSD).In additions it produces the tables needed by other scripts to generate assessment figures and tables.\n2 | calculates correlation measure among all predictions and produce an heatmap figure to visualize results\n3 | calculates correlation measure among performance indices and produce an heatmap figure to visualize results\n4 | calculates the pairwise significance of challenge evaluations and produce an heatmap figure\n5 | draws experimental values versus predicted values graph\n6 | calculates only PSWD10 and produce a table to identify difficut targets\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocomputingup%2Fcagi-p16-assessment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocomputingup%2Fcagi-p16-assessment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocomputingup%2Fcagi-p16-assessment/lists"}