{"id":15063513,"url":"https://github.com/nullranges/nullranges","last_synced_at":"2025-04-10T11:11:53.859Z","repository":{"id":45178772,"uuid":"322713837","full_name":"nullranges/nullranges","owner":"nullranges","description":"Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one or more covariates (matchRanges).","archived":false,"fork":false,"pushed_at":"2025-04-02T12:03:19.000Z","size":28752,"stargazers_count":27,"open_issues_count":4,"forks_count":5,"subscribers_count":4,"default_branch":"devel","last_synced_at":"2025-04-02T12:29:06.019Z","etag":null,"topics":["bioconductor","bootstrap","genomics","matching","statistics"],"latest_commit_sha":null,"homepage":"https://nullranges.github.io/nullranges","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/nullranges.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2020-12-18T21:59:59.000Z","updated_at":"2025-04-02T11:48:16.000Z","dependencies_parsed_at":"2024-09-25T00:03:59.960Z","dependency_job_id":"e13a071b-f62f-4955-aa0c-e98b3d63d8dc","html_url":"https://github.com/nullranges/nullranges","commit_stats":{"total_commits":427,"total_committers":11,"mean_commits":38.81818181818182,"dds":0.4285714285714286,"last_synced_commit":"aa4da4b85936a266eb1ef3d339dd0daac513c780"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nullranges%2Fnullranges","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nullranges%2Fnullranges/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nullranges%2Fnullranges/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nullranges%2Fnullranges/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nullranges","download_url":"https://codeload.github.com/nullranges/nullranges/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248208563,"owners_count":21065202,"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":["bioconductor","bootstrap","genomics","matching","statistics"],"created_at":"2024-09-25T00:03:36.035Z","updated_at":"2025-04-10T11:11:53.833Z","avatar_url":"https://github.com/nullranges.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nullranges \u003cimg id=\"nullranges_logo\" src=\"man/figures/logo.png\" align=\"right\" width=\"125\"/\u003e\n\n[![R build status](https://github.com/nullranges/nullranges/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/nullranges/nullranges/actions/workflows/check-bioc.yml)\n\n## Generation of null ranges via bootstrapping or covariate matching\n\nModular package for generation of sets of genomic features\nrepresenting the null hypothesis. These can take the form of block\nbootstrap samples of ranges using the framework of Bickel et al 2010,\nor sets of control ranges that are matched across one or more\ncovariates with a focal set. *nullranges* is designed to be\ninter-operable with other packages for analysis of genomic overlap\nenrichment, including the *plyranges* Bioconductor package.\n\nAn overview vignette can be found at the `Get started` tab above,\nincluding a **decision tree** informing which type of methods may be\nmost appropriate, whether *matching* or *bootstrapping*.\n\nDetailed vignettes on matching or bootstrapping can be found under\n`Articles`. The `Reference` tab lists function help pages. \n\n## Installation\n\nThis package can be installed via Bioconductor:\n\n```\nBiocManager::install(\"nullranges\")\n```\n\nInstalling nullranges and all of its dependencies on Mac or Windows\nwith binaries will be very fast (a minute or so).\n\nFor installing on Ubuntu, note that many *nullranges* packages are\navailable as binaries, which greatly speeds up installation.\nFollow the instructions for \n[r2u](https://eddelbuettel.github.io/r2u/), \nthen install the following via `apt`:\n\n```\nr-cran-tidyverse r-cran-ks r-cran-speedglm r-cran-data.table \nr-cran-progress r-cran-ggridges r-cran-biocmanager \nr-bioc-rtracklayer r-bioc-genomicalignments r-bioc-interactionset\n```\n\n## Papers\n\n*matchRanges* paper:\n\nEric S. Davis, Wancen Mu, Stuart Lee, Mikhail G. Dozmorov,\nMichael I. Love, Douglas H. Phanstiel. (2023)\n\"matchRanges: Generating null hypothesis genomic ranges\nvia covariate-matched sampling.\"\n*Bioinformatics*\n[doi: 10.1093/bioinformatics/btad197](https://doi.org/10.1093/bioinformatics/btad197)\n\n*bootRanges* paper:\n\nWancen Mu, Eric S. Davis, Stuart Lee, Mikhail G. Dozmorov,\nDouglas H. Phanstiel, Michael I. Love.\n(2023) \"bootRanges: Flexible generation of null sets\nof genomic ranges for hypothesis testing.\"\n*Bioinformatics*\n[doi: 10.1093/bioinformatics/btad190](https://doi.org/10.1093/bioinformatics/btad190)\n\n## Tidy Ranges Tutorial\n\nAdditional tutorial material for performing\n[tidy ranges](https://tidyomics.github.io/tidy-ranges-tutorial)\nanalysis is currently being developed.\n\n## Funding\n\nThis work was funded by the Chan Zuckerberg Initiative as part of the\nEOSS grants.\n\n![](man/figures/czi.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnullranges%2Fnullranges","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnullranges%2Fnullranges","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnullranges%2Fnullranges/lists"}