{"id":16731305,"url":"https://github.com/mikelove/alpine","last_synced_at":"2025-09-17T15:31:34.908Z","repository":{"id":11722233,"uuid":"14243756","full_name":"mikelove/alpine","owner":"mikelove","description":"Modeling and correcting fragment sequence bias for RNA-seq","archived":false,"fork":false,"pushed_at":"2024-06-04T22:40:54.000Z","size":1353,"stargazers_count":24,"open_issues_count":3,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-12-28T12:25:28.537Z","etag":null,"topics":["bioconductor","rnaseq"],"latest_commit_sha":null,"homepage":"http://biorxiv.org/content/early/2015/08/28/025767","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/mikelove.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"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}},"created_at":"2013-11-08T20:36:17.000Z","updated_at":"2024-06-04T22:40:57.000Z","dependencies_parsed_at":"2024-06-11T22:00:44.522Z","dependency_job_id":null,"html_url":"https://github.com/mikelove/alpine","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikelove%2Falpine","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikelove%2Falpine/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikelove%2Falpine/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikelove%2Falpine/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mikelove","download_url":"https://codeload.github.com/mikelove/alpine/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":233401681,"owners_count":18670811,"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","rnaseq"],"created_at":"2024-10-12T23:36:34.667Z","updated_at":"2025-09-17T15:31:29.611Z","avatar_url":"https://github.com/mikelove.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# alpine\n\n![alpine](http://mikelove.nfshost.com/img/alpine.jpg)\n\n(the [Sassolungo](https://en.wikipedia.org/wiki/Langkofel) mountain in the Dolomites)\n\n*alpine* is an R/Bioconductor package for modeling and correcting fragment\nsequence bias for RNA-seq transcript abundance estimation. In\nparticular, it is the first method of its kind to take into account\nsample-specific dependence of RNA-seq fragments on their GC content.\n\nAn example workflow can be found in `vignettes/alpine.Rmd`, or by typing:\n\n```{r}\nvignette(\"alpine\")\n```\n\n*alpine* is designed for un-stranded paired-end RNA-seq data.\n\nA paper explaining the *alpine* methods was published in December 2016:\n\n\u003chttp://dx.doi.org/10.1038/nbt.3682\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikelove%2Falpine","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmikelove%2Falpine","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikelove%2Falpine/lists"}