Orchestrating Spatial Transcriptomics Analysis with Bioconductor

Overview

This repository contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book. The online version of the book is available at https://bioconductor.org/books/OSTA/

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HL Crowell*°, Y Dong*, I Billato, P Cai, M Emons, S Gunz, B Guo, M Li, A Mahmoud, A Manukyan, H Pagès, P Panwar, S Rao, CJ Sargeant, L Shepherd Kern, M Ramos, J Sun, M Totty, VJ Carey, Y Chen, L Collado-Torres, S Ghazanfar, KD Hansen, K Martinowich, KR Maynard, E Patrick, D Righelli, D Risso, S Tiberi, L Waldron, R Gottardo†°, MD Robinson†°, SC Hicks†°, LM Weber†°. Orchestrating spatial transcriptomics analysis with Bioconductor. bioRxiv (2025). doi:10.1101/2025.11.20.688607

(* co-first. † co-senior. ° correspondence.)

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For developers

GitHub Actions

The book is built by the GitHub Actions workflows in .github/workflows/.

The GitHub Actions workflows are split into two files:

• depbuild.yml installs dependencies and stores these in a Docker image (triggered only if there are changes to DESCRIPTION or deps.Dockerfile)
• biocbook.yml builds the book and runs checks (triggered by changes to any other files)

A new public version of the book is deployed if changes are pushed to devel branch.

Pull requests

Please 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.

Local build

To 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:

setwd("inst")
quarto::quarto_render(cache = TRUE)

To 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.