{"id":20425068,"url":"https://github.com/databio/genomicdistributions","last_synced_at":"2025-09-10T00:47:57.345Z","repository":{"id":40558409,"uuid":"120372387","full_name":"databio/GenomicDistributions","owner":"databio","description":"Calculate and plot distributions of genomic ranges","archived":false,"fork":false,"pushed_at":"2025-04-23T19:48:14.000Z","size":9733,"stargazers_count":26,"open_issues_count":11,"forks_count":10,"subscribers_count":15,"default_branch":"devel","last_synced_at":"2025-04-23T20:35:28.185Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://code.databio.org/GenomicDistributions","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/databio.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","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":"2018-02-05T22:54:09.000Z","updated_at":"2025-04-23T19:42:53.000Z","dependencies_parsed_at":"2023-01-22T21:30:51.390Z","dependency_job_id":"2752f7fa-5fdb-425e-b7dd-db47f9472eb2","html_url":"https://github.com/databio/GenomicDistributions","commit_stats":null,"previous_names":[],"tags_count":41,"template":false,"template_full_name":null,"purl":"pkg:github/databio/GenomicDistributions","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FGenomicDistributions","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FGenomicDistributions/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FGenomicDistributions/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FGenomicDistributions/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/GenomicDistributions/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FGenomicDistributions/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274390719,"owners_count":25276408,"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","status":"online","status_checked_at":"2025-09-09T02:00:10.223Z","response_time":80,"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":[],"created_at":"2024-11-15T07:12:10.393Z","updated_at":"2025-09-10T00:47:57.312Z","avatar_url":"https://github.com/databio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"| Master | Dev |\n|--------|-----|\n|[![Build Status](https://travis-ci.org/databio/GenomicDistributions.svg?branch=master)](https://travis-ci.org/databio/GenomicDistributions) | [![Build Status](https://travis-ci.org/databio/GenomicDistributions.svg?branch=dev)](https://travis-ci.org/databio/GenomicDistributions) |\n\n\n\n# GenomicDistributions\n\nAn R package that provides functions for 1) calculating and 2) visualizing a variety of statistics for a collection of genomic ranges. If you have a set of genomic ranges, such as a BED file the GenomicDistributions R package can help you to explore, annotate, visualize,and compare it.\n\n## Installing\n\n### Main package\n\nWith Bioconductor:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"GenomicDistributions\")\n```\n\nOr from GitHub:\n\n```r\ndevtools::install_github(\"databio/GenomicDistributions\")\n```\n\n### Data package\n\n[GenomicDistributionsData](https://github.com/databio/GenomicDistributionsData): includes full data files, too large to include in GenomicDistributions\n\n\n## Quick start\n\nSee the vignettes for more information: http://code.databio.org/GenomicDistributions\n\n## Building long vignettes\n\nIn the [long_vignettes](/long_vignettes) are vignettes that require large external data and take a long time to run. Therefore, they should be pre-built. You can render them manually by running [long_vignettes/render-long-vignettes.R](long_vignettes/render-long-vignettes.R). This will use `knitr` to run the vignette and put the result into the `vignettes` folder, along with output figures.\n\n**Cite GenomicDistributions:**\\\nKupkova K., Mosquera J.V., Smith J.P., Stolarczyk M, Danehy T., Lawson J.T., Rogers S., LeRoy N., Sheffield N.C. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. *BMC Genomics* 23, 299 (2022). https://doi.org/10.1186/s12864-022-08467-y\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fgenomicdistributions","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fgenomicdistributions","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fgenomicdistributions/lists"}