{"id":41889358,"url":"https://github.com/rustcodepro/varpred","last_synced_at":"2026-01-25T13:38:24.412Z","repository":{"id":329343500,"uuid":"1118771635","full_name":"rustcodepro/varpred","owner":"rustcodepro","description":"a variant count approach to predict variant","archived":false,"fork":false,"pushed_at":"2025-12-18T22:39:16.000Z","size":40,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-12-21T22:48:31.473Z","etag":null,"topics":["bioinformatics","deep-learning","machine-learning","variant-analysis","variants"],"latest_commit_sha":null,"homepage":"","language":"Rust","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/rustcodepro.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-12-18T08:57:41.000Z","updated_at":"2025-12-18T22:39:20.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/rustcodepro/varpred","commit_stats":null,"previous_names":["rustcodepro/varpred"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/rustcodepro/varpred","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fvarpred","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fvarpred/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fvarpred/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fvarpred/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rustcodepro","download_url":"https://codeload.github.com/rustcodepro/varpred/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fvarpred/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28753519,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-25T10:25:12.305Z","status":"ssl_error","status_checked_at":"2026-01-25T10:25:11.933Z","response_time":113,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","deep-learning","machine-learning","variant-analysis","variants"],"created_at":"2026-01-25T13:38:24.323Z","updated_at":"2026-01-25T13:38:24.396Z","avatar_url":"https://github.com/rustcodepro.png","language":"Rust","readme":"# varpred\n\n- a variant count approach to predict variant. \n- based on expression values, number of the predicted alt alleles and sequence content. \n- Why this: \n    1. Takes into account the variant associated gene sequence features for machine learning.\n    2. Any ref allele can have multiple alt allele so convert the alt allele count into a number of the predicted alt allele for feature engineering. \n    3. Quality value as the input vector and the classification. \n    4. The ref allele is always a single allele so the frequency of the same. \n- This allows you to link the expression of the pathogenic experiment to the predicted variant and classify them to others as pathogenic or not. \n- Taking into account all the features including the sequence features ones. \n\n```\ncargo build\n```\n```\nvariant logistic classifier\n       ************************************************\n       Gaurav Sablok,\n       Email: codeprog@icloud.com\n      ************************************************\n\nUsage: varpred \u003cCOMMAND\u003e\n\nCommands:\n  classifier  Classify a entire population\n  help        Print this message or the help of the given subcommand(s)\n\nOptions:\n  -h, --help     Print help\n  -V, --version  Print version\nvarpred on  main is  0.1.0 \n❯ ./target/debug/varpred classifier -h\nClassify a entire population\n\nUsage: varpred classifier \u003cGTFFILE\u003e \u003cVCFFILE\u003e \u003cEXPRESSIONVALUES\u003e \u003cGENESFASTAINPUT\u003e \u003cQUALITYTHRESHOLDINPUT\u003e \u003cEXPRESSIONPREDINPUT\u003e \u003cTHREAD\u003e\n\nArguments:\n  \u003cGTFFILE\u003e                input path to the gtf annotation\n  \u003cVCFFILE\u003e                input path to the vcf annotation\n  \u003cEXPRESSIONVALUES\u003e       input path to the expression values\n  \u003cGENESFASTAINPUT\u003e        genes fasta file\n  \u003cQUALITYTHRESHOLDINPUT\u003e  quality threshold\n  \u003cEXPRESSIONPREDINPUT\u003e    expression prediction file\n  \u003cTHREAD\u003e                 threads for the analysis\n\nOptions:\n  -h, --help  Print help\n```\n\nGaurav Sablok \\\ncodeprog@icloud.com\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fvarpred","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frustcodepro%2Fvarpred","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fvarpred/lists"}