{"id":24890435,"url":"https://github.com/lmweber/osta","last_synced_at":"2026-01-26T18:56:01.469Z","repository":{"id":38890085,"uuid":"270734019","full_name":"lmweber/OSTA","owner":"lmweber","description":"\"Orchestrating Spatial Transcriptomics Analysis with Bioconductor\" (OSTA) online 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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":["analysis-workflows","bioconductor","spatial-transcriptomics","spatially-resolved-transcriptomics"],"created_at":"2025-02-01T17:15:40.437Z","updated_at":"2026-01-26T18:56:01.462Z","avatar_url":"https://github.com/lmweber.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"inst/images/carousel/02_OSTA.png\" width=\"25%\" align=\"right\"/\u003e \n\n# Orchestrating Spatial Transcriptomics Analysis with Bioconductor\n\n[![biocbook](https://img.shields.io/github/actions/workflow/status/lmweber/OSTA/biocbook.yml?label=Book%20build)](https://github.com/lmweber/OSTA/actions/workflows/biocbook.yml)  \n[![depbuild](https://img.shields.io/github/actions/workflow/status/lmweber/OSTA/depbuild.yml?label=Dependencies%20build)](https://github.com/lmweber/OSTA/actions/workflows/depbuild.yml)\n\n## Overview\n\nThis repository contains source files for the \"Orchestrating Spatial Transcriptomics Analysis with Bioconductor\" book.\nThe online version of the book is available at https://bioconductor.org/books/OSTA/\n\n***\n\nHL Crowell\\*°, Y Dong\\*, I Billato, P Cai, M Emons, S Gunz, B Guo, \nM Li, A Mahmoud, A Manukyan, H Pagès, P Panwar, S Rao, CJ Sargeant, L Shepherd Kern, \nM Ramos, J Sun, M Totty, VJ Carey, Y Chen, L Collado-Torres, S Ghazanfar, KD Hansen, \nK Martinowich, KR Maynard, E Patrick, D Righelli, D Risso, S Tiberi, L Waldron, \nR Gottardo†°, MD Robinson†°, SC Hicks†°, LM Weber†°.\nOrchestrating spatial transcriptomics analysis with Bioconductor. *bioRxiv* (2025). \n[doi:10.1101/2025.11.20.688607](http://doi.org/10.1101/2025.11.20.688607)\n\n(\\* co-first. † co-senior. ° correspondence.)\n\n***\n\n## For developers\n\n### GitHub Actions\n\nThe book is built by the GitHub Actions workflows in `.github/workflows/`.\n\nThe GitHub Actions workflows are split into two files:\n- `depbuild.yml` installs dependencies and stores these in a Docker image (triggered only if there are changes to `DESCRIPTION` or `deps.Dockerfile`)\n- `biocbook.yml` builds the book and runs checks (triggered by changes to any other files)\n\nA new public version of the book is deployed if changes are pushed to `devel` branch.\n\n\n### Pull requests\n\nPlease send pull requests into `sandbox` branch (instead of `devel`). This will trigger GitHub Actions to build the book and run checks, but will not deploy a new version of the book. The maintainers will then merge into `devel` to deploy a new version of the book after reviewing and accepting the pull request.\n\n\n### Local build\n\nTo build a local version of the book, first install all dependency packages (from `DESCRIPTION`) manually. Then, run `quarto_render()` in an R session in the `inst/` directory as follows:\n\n```\nsetwd(\"inst\")\nquarto::quarto_render(cache = TRUE)\n```\n\nTo compile a complete fresh local build, delete all existing build files by deleting the following directories and files: `inst/.quarto/`, `inst/docs/`, `inst/index_cache/`, any files and directories except `.qmd` files and `images/` directory in `inst/pages/` (e.g. directory names ending with `_cache/` or `_files/`, `.md` files, and `.rds` files). You may also need to empty the `BiocFileCache` cache directory if any data files stored in the OSF data repository have changed.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flmweber%2Fosta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flmweber%2Fosta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flmweber%2Fosta/lists"}