{"id":51388798,"url":"https://github.com/alextkalinka/delboy","last_synced_at":"2026-07-03T21:37:21.468Z","repository":{"id":43453132,"uuid":"293352397","full_name":"alextkalinka/delboy","owner":"alextkalinka","description":"Differential-representation analysis by Elastic-net Logistic regression with BinOmial-thinning validitY tests","archived":false,"fork":false,"pushed_at":"2022-07-03T19:22:45.000Z","size":440,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2023-03-11T06:11:27.251Z","etag":null,"topics":["differential-expression","r-package","rna-seq"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alextkalinka.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":"2020-09-06T19:59:14.000Z","updated_at":"2022-01-26T14:29:55.000Z","dependencies_parsed_at":"2022-09-23T05:24:49.597Z","dependency_job_id":null,"html_url":"https://github.com/alextkalinka/delboy","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"purl":"pkg:github/alextkalinka/delboy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alextkalinka%2Fdelboy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alextkalinka%2Fdelboy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alextkalinka%2Fdelboy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alextkalinka%2Fdelboy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alextkalinka","download_url":"https://codeload.github.com/alextkalinka/delboy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alextkalinka%2Fdelboy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35102741,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-03T02:00:05.635Z","response_time":110,"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":["differential-expression","r-package","rna-seq"],"created_at":"2026-07-03T21:37:19.156Z","updated_at":"2026-07-03T21:37:21.464Z","avatar_url":"https://github.com/alextkalinka.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# `delboy`\n\n## Summary\n\n`delboy` is an `R` package for conducting differential-expression analyses on RNA-seq data in which there are exactly **two groups** to be contrasted. The method is designed to improve sensitivity for under-powered data-sets, in which the effect sizes are small and there are few replicates, while controlling the False Discovery Rate (FDR).\n\n`delboy` - **D**ifferential-representation analysis by **E**lastic-net **L**ogistic regression with **B**in**O**mial-thinning validit**Y** tests.\n\nYou can read about the method in the companion [manuscript](https://www.biorxiv.org/content/10.1101/2020.10.15.340737v1.full).\n\n## Installation\n\n```r\n# install.packages(\"devtools\")\ndevtools::install_github(\"alextkalinka/delboy\")\n```\n\n## Usage\n\nInput data should be a data frame of normalized counts in which there is a gene column with the remaining columns being sample columns.\n\n```r\ndb \u003c- delboy::run_delboy(\n\t\tdata = expr_data_frame,\n\t\tgroup_1 = c(\"ctrl-1\",\"ctrl-2\",\"ctrl-3\"),\n\t\tgroup_2 = c(\"treat-1\",\"treat-2\",\"treat-3\"),\n\t\tfilter_cutoff = 40,\n\t\tgene_column = \"gene_id\",\n\t\tbatches = NULL\n)\n\n# To print a summary report to the console:\ndb\n\n# To extract a data frame of hits\n# (includes a 'Predicted_False_Positive' column):\nmy_hits \u003c- delboy::hits(db)\n\n```\n\nTo plot validation performance next to original data showing the false-positive decision boundary (axes limits can be controlled using the `xlim` and `ylim` arguments):\n\n```r\nplot(db, type = \"lfc_expr\")\n```\n\nTo visualize false negatives in the validation data relative to the false-positive decision boundary:\n\n```r\nplot(db, type = \"lfc_expr_FN\")\n```\n\nTo plot the distrubution of log-fold changes used for the validation data:\n\n```r\nplot(db, type = \"lfc_nonnull\")\n```\n\n## References\n\nKalinka, A. T. (2020). Improving the sensitivity of differential-expression analyses for under-powered RNA-seq experiments. bioRxiv [10.1101/2020.10.15.340737](https://www.biorxiv.org/content/10.1101/2020.10.15.340737v1.full).\n\n## Bugs, Issues, or Requests\n\nPlease contact [Alex Kalinka](mailto:alex.t.kalinka@gmail.com).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falextkalinka%2Fdelboy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falextkalinka%2Fdelboy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falextkalinka%2Fdelboy/lists"}