{"id":32615693,"url":"https://github.com/stemangiola/bioc2021_tidytranscriptomics","last_synced_at":"2026-02-26T19:32:40.214Z","repository":{"id":47561925,"uuid":"343062488","full_name":"stemangiola/bioc2021_tidytranscriptomics","owner":"stemangiola","description":null,"archived":false,"fork":false,"pushed_at":"2021-08-24T00:07:46.000Z","size":45210,"stargazers_count":3,"open_issues_count":3,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-07-22T00:15:36.840Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Dockerfile","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/stemangiola.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-02-28T09:08:21.000Z","updated_at":"2023-11-19T13:17:15.000Z","dependencies_parsed_at":"2022-07-25T04:46:11.600Z","dependency_job_id":null,"html_url":"https://github.com/stemangiola/bioc2021_tidytranscriptomics","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/stemangiola/bioc2021_tidytranscriptomics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stemangiola%2Fbioc2021_tidytranscriptomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stemangiola%2Fbioc2021_tidytranscriptomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stemangiola%2Fbioc2021_tidytranscriptomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stemangiola%2Fbioc2021_tidytranscriptomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stemangiola","download_url":"https://codeload.github.com/stemangiola/bioc2021_tidytranscriptomics/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stemangiola%2Fbioc2021_tidytranscriptomics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29868539,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-26T18:42:30.764Z","status":"ssl_error","status_checked_at":"2026-02-26T18:41:47.936Z","response_time":89,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":[],"created_at":"2025-10-30T16:42:48.025Z","updated_at":"2026-02-26T19:32:40.207Z","avatar_url":"https://github.com/stemangiola.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![DOI](https://zenodo.org/badge/343062488.svg)](https://zenodo.org/badge/latestdoi/343062488)\n[![.github/workflows/basic_checks.yaml](https://github.com/stemangiola/bioc2021_tidytranscriptomics/workflows/.github/workflows/basic_checks.yaml/badge.svg)](https://github.com/stemangiola/bioc2021_tidytranscriptomics/actions) [![Docker](https://github.com/Bioconductor/BioC2020/raw/master/docs/images/docker_icon.png)](https://hub.docker.com/repository/docker/stemangiola/bioc2021_tidytranscriptomics) \t\n\u003c!-- badges: end --\u003e\n\n# Introduction to Tidy Transcriptomics\n\u003cp float=\"left\"\u003e\n\u003cimg height=\"100\" alt=\"bioc2021\" src=\"https://github.com/Bioconductor/BiocStickers/blob/71e4c2cb323c441daa0f2f9d48d3b8bbb564a3e2/events/Bioc2021/BioC2021.png?raw=true\"/\u003e\n\u003cimg height=\"100\" alt=\"tidybulk\" src=\"https://github.com/Bioconductor/BiocStickers/blob/master/tidybulk/tidybulk.png?raw=true\"/\u003e\n\u003c/p\u003e\n\n## Instructor names and contact information\n\n* Maria Doyle \u003cMaria.Doyle at petermac.org\u003e  \n* Stefano Mangiola \u003cmangiola.s at wehi.edu.au\u003e\n\n## Syllabus\n\nMaterial [web page](https://stemangiola.github.io/bioc2021_tidytranscriptomics/articles/tidytranscriptomics.html).\n\nMore details on the workshop are below.\n\n## Workshop package installation \n\nThis is necessary in order to reproduce the code shown in the workshop. The workshop is designed for R `4.1` and can be installed using one of the two ways below.\n\n### Via Docker image\n\nIf you're familiar with [Docker](https://docs.docker.com/get-docker/) you could use the Docker image which has all the software pre-configured to the correct versions.\n\n```\ndocker run -e PASSWORD=abc -p 8787:8787 stemangiola/bioc2021_tidytranscriptomics:bioc2021\n```\n\nOnce running, navigate to \u003chttp://localhost:8787/\u003e and then login with\n`Username:rstudio` and `Password:abc`.\n\nYou should see the Rmarkdown file with all the workshop code which you can run.\n\n### Via GitHub\n\nAlternatively, you could install the workshop using the commands below in R `4.1`.\n\n```\n#install.packages('remotes')\n\n# Need to set this to prevent installation erroring due to even tiny warnings, similar to here: https://github.com/r-lib/remotes/issues/403#issuecomment-748181946\nSys.setenv(\"R_REMOTES_NO_ERRORS_FROM_WARNINGS\" = \"true\")\n\n# Install same versions used in the workshop\nremotes::install_github(c(\"stemangiola/tidybulk@v1.4.0\"\", \"stemangiola/tidySummarizedExperiment@v1.2.0\", \"stemangiola/tidySingleCellExperiment@v1.3.0\"))\n\n# Install workshop package\nremotes::install_github(\"stemangiola/bioc2021_tidytranscriptomics\", build_vignettes = TRUE)\n\n# To view vignettes\nlibrary(bioc2021tidytranscriptomics)\nbrowseVignettes(\"bioc2021tidytranscriptomics\")\n```\n\nTo run the code, you could then copy and paste the code from the workshop vignette or [R markdown file](https://raw.githubusercontent.com/stemangiola/bioc2021_tidytranscriptomics/master/vignettes/tidytranscriptomics.Rmd) into a new R Markdown file on your computer.\n\n## Workshop Description\n\nRecently, [plyranges](https://bioconductor.org/packages/release/bioc/html/plyranges.html) and [tidybulk](https://www.bioconductor.org/packages/release/bioc/html/tidybulk.html) have made efforts toward the harmonization of biological data structures and workflows using the concept of data tidiness, to facilitate modularisation. In this workshop, we present [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) and [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/), two R packages that allow the user to visualise and manipulate SingleCellExperiment and SummarizedExperiment objects in a tidy fashion. Importantly, the tidybulk framework now works natively with SummarizedExperiment objects and, thanks to tidySummarizedExperiment, allows tidy and modular RNA sequencing analyses without renouncing the efficiency of Bioconductor data containers. These tools are part of the [tidytranscriptomics](https://github.com/stemangiola/tidytranscriptomics) R software suite, and represent an effort toward the harmonisation of transcriptional analyses under the tidy umbrella.\n\n### Pre-requisites\n\n* Some familiarity with tidyverse syntax\n* Some familiarity with bulk RNA-seq and single cell RNA-seq\n\nRecommended Background Reading\n[Introduction to R for Biologists](https://melbournebioinformatics.github.io/r-intro-biologists/intro_r_biologists.html)\n\n### Workshop Participation\n\nThe workshop format is a 1.5 hour session consisting of hands-on demos, challenges and Q\u0026A.\n\n### _R_ / _Bioconductor_ packages used\n\n* tidySummarizedExperiment\n* tidySingleCellExperiment\n* tidybulk\n* tidyHeatmap\n* limma\n* edgeR\n* DESeq2\n* airway\n* org.Hs.eg.db\n* dittoSeq\n* ggrepel\n* GGally\n* plotly\n\n\n### Time outline\n\nGuide\n\n| Activity - Hands on demos with Q\u0026A                                 | Time |\n|--------------------------------------------------------------------|------|\n| Part 1 Bulk RNA-seq with tidySummarizedExperiment and tidybulk     |  45  |\n| Part 2 Single-cell RNA-seq with tidySingleCellExperiment           |  45  |\n| Total                                                              |  90m |\n\n\n#### Learning goals\n\n* To understand how transcriptomic data can be represented and analysed according to the tidy data paradigm with tidySummarizedExperiment, tidybulk and tidySingleCellExperiment.\n\n#### Learning objectives\n* Explore, visualise and analyse bulk RNA-seq count data with tidySummarizedExperiment and tidybulk\n* Explore and visualise single cell RNA-seq count data with tidySingleCellExperiment\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstemangiola%2Fbioc2021_tidytranscriptomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstemangiola%2Fbioc2021_tidytranscriptomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstemangiola%2Fbioc2021_tidytranscriptomics/lists"}