{"id":17403709,"url":"https://github.com/gagneurlab/outrider","last_synced_at":"2025-05-08T04:40:34.749Z","repository":{"id":32420148,"uuid":"126519438","full_name":"gagneurlab/OUTRIDER","owner":"gagneurlab","description":"OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data","archived":false,"fork":false,"pushed_at":"2025-04-13T20:13:50.000Z","size":11711,"stargazers_count":52,"open_issues_count":15,"forks_count":11,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-05-05T09:58:40.882Z","etag":null,"topics":["count-data","diagnostics","expression-analysis","mendelian-genetics","outlier-detection","r","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gagneurlab.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,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2018-03-23T17:42:32.000Z","updated_at":"2025-05-02T08:07:24.000Z","dependencies_parsed_at":"2023-10-11T08:59:15.959Z","dependency_job_id":"d2320ebd-94d7-405f-8c9a-a8f222c2bc37","html_url":"https://github.com/gagneurlab/OUTRIDER","commit_stats":{"total_commits":416,"total_committers":18,"mean_commits":23.11111111111111,"dds":"0.44471153846153844","last_synced_commit":"067853af44effc99897a98bd3221baf7ea612e92"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FOUTRIDER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FOUTRIDER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FOUTRIDER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FOUTRIDER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gagneurlab","download_url":"https://codeload.github.com/gagneurlab/OUTRIDER/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253002778,"owners_count":21838634,"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":["count-data","diagnostics","expression-analysis","mendelian-genetics","outlier-detection","r","rna-seq"],"created_at":"2024-10-16T19:07:20.841Z","updated_at":"2025-05-08T04:40:34.718Z","avatar_url":"https://github.com/gagneurlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OUTRIDER #\n[![Build](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml)\n[![Version](https://img.shields.io/github/v/release/gagneurlab/OUTRIDER)](https://github.com/gagneurlab/OUTRIDER/releases)\n[![Coverage status](https://codecov.io/gh/gagneurlab/OUTRIDER/branch/master/graph/badge.svg)](https://codecov.io/github/gagneurlab/OUTRIDER?branch=master)\n[![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/gagneurlab/OUTRIDER/blob/master/LICENSE)\n\nOUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples.\nThe method is published in the [AJHG](https://doi.org/10.1016/j.ajhg.2018.10.025)\nand available through [Bioconductor](http://bioconductor.org/packages/release/bioc/html/OUTRIDER.html).\nIt is also part of the workflow [DROP](https://github.com/gagneurlab/drop), which is described in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5).\n\nPlease cite our method paper if you use it in a publication:\n\n\u003e Brechtmann F, Mertes C, Matusevičiūtė A, *et al.* OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. *Am J Hum Genet. 2018;103(6):907-917*. https://doi.org/10.1016/j.ajhg.2018.10.025\n\n\n## Installation\n\n`OUTRIDER` is an R software package requiring a running [R 3.6 version or higher](https://cran.r-project.org/).\n\nWe will use `BiocManager` to install the package and its dependencies. If you\nwant to install the devel version of `OUTRIDER`, please install it \nwith devtools from GitHub directly [(see below)](#OUTRIDER-development-installation).\n\n\n```\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install('OUTRIDER')\n```\n\nIf you have dependency issues while installing any package, please have a look\nat the Troubleshooting section or submit an issue on [GitHub](https://github.com/gagneurlab/OUTRIDER/issues).\n\n### OUTRIDER development installation\n\nIf you want to get the latest\ndevelopment version of `OUTRIDER`, you can install it from GitHub with\n`devtools`. For this, you need a working development environment to compile the\nC++ code (see for details: [Windows](https://cran.r-project.org/bin/windows/Rtools/)\nor [MacOS X](https://cran.r-project.org/bin/macosx/tools/)).\n\n```\ninstall.packages('devtools')\n\n# latest development version\ndevtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)\n\n# installing a specific version/tag of OUTRIDER\ndevtools::install_github('gagneurlab/OUTRIDER@1.20.1', dependencies=TRUE)\n```\n\nTo check which versions/tags are available you can check the GitHub repo\n[here](https://github.com/gagneurlab/OUTRIDER/releases).\n\n### Quick tour through OUTRIDER\n\nTo get started with `OUTRIDER`, please have a look at our\n[vignette](http://bioconductor.org/packages/release/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf).\nIn order to get the pdf version, please type the following code in an R session:\n\n```\nlibrary(OUTRIDER)\nvignette('OUTRIDER')\n```\n\n### Toubleshooting\n\n#### Missing libraries while compiling R packages\n\nOn some Linux distributions we need the developer libraries for compiling the R packages.\n\nTo install those packages, please run as administrator: \n\nFor Ubuntu or debian based systems:\n```\nsudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmariadbd-dev\n```\n\nFor centOS or RHEL based systems:\n```\nsudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgagneurlab%2Foutrider","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgagneurlab%2Foutrider","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgagneurlab%2Foutrider/lists"}