{"id":14067700,"url":"https://github.com/variani/finemapr","last_synced_at":"2026-01-18T04:14:59.609Z","repository":{"id":144780894,"uuid":"120934279","full_name":"variani/finemapr","owner":"variani","description":"Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF","archived":false,"fork":false,"pushed_at":"2025-06-17T19:21:35.000Z","size":1263,"stargazers_count":32,"open_issues_count":8,"forks_count":13,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-30T02:59:16.199Z","etag":null,"topics":["caviar","fine-mapping","finemap","paintor","rpackage","rstats"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/variani.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}},"created_at":"2018-02-09T17:19:05.000Z","updated_at":"2025-07-26T00:39:13.000Z","dependencies_parsed_at":null,"dependency_job_id":"870a7198-eb0c-457c-923d-d4e7652b4f7f","html_url":"https://github.com/variani/finemapr","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/variani/finemapr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/variani%2Ffinemapr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/variani%2Ffinemapr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/variani%2Ffinemapr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/variani%2Ffinemapr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/variani","download_url":"https://codeload.github.com/variani/finemapr/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/variani%2Ffinemapr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28529467,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T00:39:45.795Z","status":"online","status_checked_at":"2026-01-18T02:00:07.578Z","response_time":98,"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":["caviar","fine-mapping","finemap","paintor","rpackage","rstats"],"created_at":"2024-08-13T07:05:44.015Z","updated_at":"2026-01-18T04:14:59.592Z","avatar_url":"https://github.com/variani.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"# finemapr\n\n[![travis-ci build status](https://travis-ci.org/variani/finemapr.svg?branch=master)](https://travis-ci.org/variani/finemapr)\n\n![](misc/figures/finemap-2causal.png)\n\nR interface to fine-mappers:\n\n- FINEMAP http://www.christianbenner.com/\n- CAVIAR https://github.com/fhormoz/caviar\n- PAINTOR https://github.com/gkichaev/PAINTOR_V3.0\n\nBy using `finemapr`, your input files are automatically prepared for each tool, the analysis workflow is tool-independent; and exploration of fine-mapping results is powered by R in printing/plotting/data export.\n\n**Note**: the package is still under development and its current version is not stable. The current work aims at switching from `run_\u003ctool\u003e` functions to a more general one, [finemapr](https://github.com/variani/finemapr/blob/master/R/finemapr.R). The later function makes use of S3 method dispatch features. Thus, use this package with caution until the stable release comes out.\n\n## Quick start\n\n```r\nlibrary(finemapr)\nlibrary(tidyverse)\n\n# get some example data\nfinemapr::example_finemap() %\u003e% attach\n\n# run finemapping, default tool is finemap\nout \u003c- finemapr(z1, ld1, n1, args = \"--n-causal-max 3\")\n\n# print \u0026 plot results\nout\n\nplot(out, grid_nrow = 1)\n```\n\n## Tool-independent analysis workflow\n\n```r\n# set up\noptions(finemapr_\u003ctool\u003e = \"\u003cpath to fine-mapping tool\u003e\")\n\n# read input files\nmy_zscores \u003c- read_zscores(\"\u003cmy_scores.tab\u003e\")\nmy_ld \u003c- read_ld(\"\u003cmy_ld.tab\u003e\")\n\n# run analysis\n# depreciated, but still works: out \u003c- run_\u003ctool\u003e(my_zscores, my_ld, args = \"\u003ccustom arguments\u003e\")\nout \u003c- finemapr(my_zscores, my_ld, method = \"\u003ctool\u003e\", args = \"\u003ccustom arguments\u003e\")\n\n# explore results\nprint(out)\nhead(out$snp) # main table of results\nplot(out)\n\n# export results\nwrite.table(out$snp, \"\u003cmy_results.tab\u003e\")\n```\n\n## Examples\n\nSee the vignette [Fine-mapping analysis pipeline by `finemapr`](https://variani.github.io/finemapr/vignettes/finemapr.html).\n\n## Related projects\n\n- [FineMapping pipeline using GWAS summary statistics](https://github.com/jinghuazhao/FM-pipeline)\n- [Finemapping pipeline that automates the usage of PAINTOR, and CAVIAR BF](https://github.com/theboocock/fine_mapping_pipeline)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvariani%2Ffinemapr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvariani%2Ffinemapr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvariani%2Ffinemapr/lists"}