{"id":22794794,"url":"https://github.com/menchelab/apobex","last_synced_at":"2025-03-30T17:44:02.678Z","repository":{"id":233933817,"uuid":"788051644","full_name":"menchelab/apobex","owner":"menchelab","description":null,"archived":false,"fork":false,"pushed_at":"2024-06-10T09:50:08.000Z","size":6783,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-05T20:01:55.184Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/menchelab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-04-17T17:26:55.000Z","updated_at":"2024-06-10T09:50:12.000Z","dependencies_parsed_at":"2024-06-10T11:04:37.440Z","dependency_job_id":null,"html_url":"https://github.com/menchelab/apobex","commit_stats":null,"previous_names":["menchelab/apobex"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/menchelab%2Fapobex","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/menchelab%2Fapobex/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/menchelab%2Fapobex/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/menchelab%2Fapobex/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/menchelab","download_url":"https://codeload.github.com/menchelab/apobex/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246357764,"owners_count":20764361,"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":[],"created_at":"2024-12-12T04:10:27.464Z","updated_at":"2025-03-30T17:44:02.654Z","avatar_url":"https://github.com/menchelab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# apobex\n\nThis repository contains all data and code to analyze and visualize the mutational data presented in:\n**\"Ubiquitin E3 ligases UBR4, UBR5 and HUWE1 protect human genome integrity by targeting cancer-associated APOBEC3 deaminases for degradation\"**\nlink to preprint: https://www.biorxiv.org/content/biorxiv/early/2024/04/26/2024.04.23.590688.full.pdf\n\n## Installation instructions\nInstallation time 1 minute\n\n#### 1. clone the GitHub repository:\n```bash\ngit clone https://github.com/menchelab/apobex.git\n```\n#### 2. Navigate into the ApobeX directory within the cloned repository\n```bash\ncd apobex #go into cloned repository\n```\n#### 3. Install the ApobeX package from the local repository:\n```R\nlibrary(devtools)\ninstall(\"ApobeX\")\n```\n#### 4. Load the ApobeX package:\n```R\nlibrary(ApobeX)\n```\n\n### Analysis\nrun notbook ../analysis/bootstrapped_background_correction.ipynb\n\n### Plotting\n\n#### figures\nrun notebook ../plotting/notbooks/3_apobex_plotting_refitting.ipynb\n\n#### signature presence test\nrun norebook ../plotting/notbooks/3_apobex_msigact.ipynb\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fapobex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmenchelab%2Fapobex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fapobex/lists"}