{"id":32110914,"url":"https://github.com/eolagbaju/oder","last_synced_at":"2026-02-21T10:31:35.057Z","repository":{"id":110030065,"uuid":"357569414","full_name":"eolagbaju/ODER","owner":"eolagbaju","description":"Optimising Definitions of Expressed Regions","archived":false,"fork":false,"pushed_at":"2021-10-08T16:13:17.000Z","size":15678,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-20T14:08:16.704Z","etag":null,"topics":["annotation","genomics","rna-seq","transcriptomics"],"latest_commit_sha":null,"homepage":"https://eolagbaju.github.io/ODER/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/eolagbaju.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-04-13T13:47:50.000Z","updated_at":"2022-10-18T12:16:38.000Z","dependencies_parsed_at":"2023-04-27T20:47:35.150Z","dependency_job_id":null,"html_url":"https://github.com/eolagbaju/ODER","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/eolagbaju/ODER","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eolagbaju%2FODER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eolagbaju%2FODER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eolagbaju%2FODER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eolagbaju%2FODER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/eolagbaju","download_url":"https://codeload.github.com/eolagbaju/ODER/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eolagbaju%2FODER/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29679049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T09:33:50.764Z","status":"ssl_error","status_checked_at":"2026-02-21T09:33:19.949Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["annotation","genomics","rna-seq","transcriptomics"],"created_at":"2025-10-20T14:06:50.258Z","updated_at":"2026-02-21T10:31:35.038Z","avatar_url":"https://github.com/eolagbaju.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# ODER\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/ODER.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/ODER)\n[![R-CMD-check-bioc](https://github.com/eolagbaju/ODER/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/eolagbaju/ODER/actions)\n[![Codecov test coverage](https://codecov.io/gh/eolagbaju/ODER/branch/master/graph/badge.svg)](https://codecov.io/gh/eolagbaju/ODER?branch=master)\n\u003c!-- badges: end --\u003e\n\nThe goal of `ODER` is to **O**ptimise the **D**efinition of **E**xpressed **R**egions. `ODER` is a packaged form of the method developed in the Zhang et al. 2020 publication: [Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders](https://www.science.org/doi/10.1126/sciadv.aay8299). For a more detailed explanation of using `ODER`, please see the [vignette](https://eolagbaju.github.io/ODER/articles/ODERflow.html). For more explanation of the methodology behind `ODER`, see the mehtods section of the  [original publication](https://www.science.org/doi/10.1126/sciadv.aay8299). \n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `ODER` using from [Bioconductor](http://bioconductor.org/) the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"ODER\")\n```\n\nAnd the development version from [GitHub](https://github.com/eolagbaju/ODER) with:\n\n```{r 'install_dev', eval = FALSE}\nBiocManager::install(\"eolagbaju/ODER\")\n```\n\n## Citation\n\nBelow is the citation output from using `citation('ODER')` in R. Please\nrun this yourself to check for any updates on how to cite __ODER__.\n\n```{r 'citation', eval = requireNamespace('ODER')}\nmessage(citation(\"ODER\"), bibtex = TRUE)\n```\n\nPlease note that the `ODER` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.\n\n## Code of Conduct\n\nPlease note that the `ODER` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.\n\n## Development tools\n\n* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.\n* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.\n* The [documentation website](http://eolagbaju.github.io/ODER) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nFor more details, check the `dev` directory.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feolagbaju%2Foder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Feolagbaju%2Foder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feolagbaju%2Foder/lists"}