This repository contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book.
The development version of the book is available at: https://lmweber.org/OSTA/
To make changes and publish an updated version of the book, first manually commit and push any changes to files that are located outside the inst/ directory, and then use the following code using the BiocBook package to commit and publish changes to files in inst/ (e.g. inst/assets/_book.yml and inst/pages/chapter-name.qmd if adding a new chapter):
library(BiocBook)
bb <- BiocBook(".")
publish(bb, message = "commit message")
To build and preview the book locally, use the following code:
library(BiocBook)
bb <- BiocBook(".")
preview(bb)
Image files are stored separately in the OSTA-resources repository and linked within chapters using URLs, in order to keep the size of the main repository smaller. Please use this repository for image files in pull requests.
This book is built using the BiocBook package, developed by Jacques Serizay for building Quarto books with Bioconductor. More details on BiocBook can be found in the BiocBook book.