{"id":13774701,"url":"https://github.com/pkimes/benchmark-fdr","last_synced_at":"2026-01-07T07:05:59.645Z","repository":{"id":49822333,"uuid":"100814197","full_name":"pkimes/benchmark-fdr","owner":"pkimes","description":"Benchmarking study of recent covariate-adjusted FDR methods","archived":false,"fork":false,"pushed_at":"2019-04-16T23:59:22.000Z","size":24497,"stargazers_count":14,"open_issues_count":0,"forks_count":5,"subscribers_count":9,"default_branch":"master","last_synced_at":"2024-02-15T11:33:27.582Z","etag":null,"topics":["benchmarking","false-discovery-rate"],"latest_commit_sha":null,"homepage":"","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/pkimes.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}},"created_at":"2017-08-19T18:37:27.000Z","updated_at":"2023-03-02T12:18:57.000Z","dependencies_parsed_at":"2022-09-14T07:10:51.818Z","dependency_job_id":null,"html_url":"https://github.com/pkimes/benchmark-fdr","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pkimes%2Fbenchmark-fdr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pkimes%2Fbenchmark-fdr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pkimes%2Fbenchmark-fdr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pkimes%2Fbenchmark-fdr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pkimes","download_url":"https://codeload.github.com/pkimes/benchmark-fdr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253528415,"owners_count":21922623,"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":["benchmarking","false-discovery-rate"],"created_at":"2024-08-03T17:01:29.428Z","updated_at":"2026-01-07T07:05:59.638Z","avatar_url":"https://github.com/pkimes.png","language":"Jupyter Notebook","funding_links":[],"categories":["Statistics"],"sub_categories":["False Discovery Rates"],"readme":"# Benchmarking Study of Covariate-Adjusted FDR Methods \n\nThis repository includes all code used to perform analyses and generate figures for the manuscript, [_A practical guide to methods controlling false discoveries in computational biology_](https://www.biorxiv.org/content/early/2018/10/31/458786). \n\n## Notes\n\nBefore attempting to run the code in this repository, please read the following notes.\n\n### Cloning\n\nWe **do not** recommond cloning this entire repository. The repository includes all historical commits and is incredibly large. Instead, we recommend either making a shallow clone of the repository using the following code.\n\n```bash\n git clone --depth=1 https://github.com/pkimes/benchmark-fdr.git\n```\n\n### SummarizedBenchmark\n\nThe code in this repository was run using an older version of the `SummarizedBenchmark` package and will not run with newer versions of the package. An older version of the package should be installed from GitHub using the following R code.\n\n```r\ndevtools::install_github(\"areyesq89/SummarizedBenchmark\", ref = \"fdrbenchmark\")\n```\n\n### Rendered reports\n\nFinal rendered `Rmd` files for simulations and case studies included in the manuscripts are available in [this repository](https://github.com/pkimes/benchmark-fdr-html), and are rendered [here](http://www.pkimes.com/benchmark-fdr-html/) via GitHub pages.\n\n## Citation\n\nKorthauer K\u0026dagger;, Kimes PK\u0026dagger;, Duvallet C\u0026Dagger;, Reyes A\u0026Dagger;, Subramanian A\u0026Dagger;, Teng M, Shukla C, Alm EJ, Hicks SC\\*.\n_A practical guide to methods controlling false discoveries in computational biology._ bioRxiv. doi: https://doi.org/10.1101/458786\n\n\u0026dagger;: co-first authors, \u0026Dagger;: co-second authors, \\*: corresponding author\n\n## License/Copyright\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![License: CC BY-NC-ND 4.0](https://img.shields.io/badge/License-CC%20BY--NC--ND%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc-nd/4.0/)  \nAll code in this project is made available under a MIT license.  \nAll non-code text in this project is made available under a CC BY-NC-ND 4.0 license.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpkimes%2Fbenchmark-fdr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpkimes%2Fbenchmark-fdr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpkimes%2Fbenchmark-fdr/lists"}