{"id":16732084,"url":"https://github.com/sa-lee/fluentgenomics","last_synced_at":"2026-01-03T05:03:10.107Z","repository":{"id":86151476,"uuid":"223296809","full_name":"sa-lee/fluentGenomics","owner":"sa-lee","description":"plyranges and tximeta case study","archived":false,"fork":false,"pushed_at":"2023-07-02T08:09:14.000Z","size":22922,"stargazers_count":7,"open_issues_count":4,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-22T08:14:38.237Z","etag":null,"topics":["atac-seq","bioconductor","genomics","rna-seq","workflow"],"latest_commit_sha":null,"homepage":"https://sa-lee.github.io/fluentGenomics/","language":"TeX","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/sa-lee.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}},"created_at":"2019-11-22T01:20:41.000Z","updated_at":"2023-07-02T07:26:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"977d3b71-3410-4fce-8203-eeded4b1d7cd","html_url":"https://github.com/sa-lee/fluentGenomics","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sa-lee%2FfluentGenomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sa-lee%2FfluentGenomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sa-lee%2FfluentGenomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sa-lee%2FfluentGenomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sa-lee","download_url":"https://codeload.github.com/sa-lee/fluentGenomics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243773318,"owners_count":20345809,"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":["atac-seq","bioconductor","genomics","rna-seq","workflow"],"created_at":"2024-10-12T23:39:48.842Z","updated_at":"2026-01-03T05:03:10.035Z","avatar_url":"https://github.com/sa-lee.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Fluent genomics with plyranges and tximeta \n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/sa-lee/fluentGenomics/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sa-lee/fluentGenomics/actions)\n\u003c!-- badges: end --\u003e\n\nIn *fluentGenomics* we explore the use of the Bioconductor packages plyranges and tximeta through integrating results from an experiment using RNA-seq and ATAC-seq data. Readers will learn how to perform genomic range based operations in a principled way using *plyranges* and how to cleanly import quantification and differential expression data into R using *tximeta*. \n\n## Installation\n\nThe `fluentGenomics` package is available on Bioconductor:\n\n```r\n# install.packages(\"BiocManager\")\nBiocManager::install('fluentGenomics')\n```\n\nTo install `fluentGenomics` from github with associated dependencies use\n\n``` r\nBiocManager::install('sa-lee/fluentGenomics', \n                     build_vignettes = TRUE,\n                     dependencies = TRUE)\n```\n\nTo install `fluentGenomics` from Bioconductor's devel branch use:\n``` r\nBiocManager::install('fluentGenomics',  version = 'devel')\n```\n\n## Workflow\n\nOnce the package has been installed, you can work through\nthe vignette directly from R/Rstudio with:\n\n``` r\nvignette(\"fluentGenomics\")\n```\n\nOr you can read it online \n[here](https://bioconductor.org/packages/devel/workflows/vignettes/fluentGenomics/inst/doc/fluentGenomics.html)\n\n## Course\n\nYou can use the package as course material directly with the `usethis`\npackage:\n\n```{r}\nusethis::use_course(\"sa-lee/fluentGenomics\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsa-lee%2Ffluentgenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsa-lee%2Ffluentgenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsa-lee%2Ffluentgenomics/lists"}