https://github.com/lmweber/osta
"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book
https://github.com/lmweber/osta
analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics
Last synced: 9 days ago
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"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book
- Host: GitHub
- URL: https://github.com/lmweber/osta
- Owner: lmweber
- Created: 2020-06-08T16:07:01.000Z (over 5 years ago)
- Default Branch: devel
- Last Pushed: 2025-11-27T17:44:04.000Z (2 months ago)
- Last Synced: 2025-11-28T02:12:42.970Z (2 months ago)
- Topics: analysis-workflows, bioconductor, spatial-transcriptomics, spatially-resolved-transcriptomics
- Language: TeX
- Homepage: https://bioconductor.org/books/OSTA/
- Size: 72.1 MB
- Stars: 102
- Watchers: 9
- Forks: 38
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# Orchestrating Spatial Transcriptomics Analysis with Bioconductor
[](https://github.com/lmweber/OSTA/actions/workflows/biocbook.yml)
[](https://github.com/lmweber/OSTA/actions/workflows/depbuild.yml)
## 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/
***
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](http://doi.org/10.1101/2025.11.20.688607)
(\* co-first. † co-senior. ° correspondence.)
***
## 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.