https://github.com/lmweber/osta

"Principles of Spatial (Transcript)omics Analysis with Bioconductor" book
https://github.com/lmweber/osta

analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: about 2 months ago
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"Principles of Spatial (Transcript)omics Analysis with Bioconductor" book

• Host: GitHub
• URL: https://github.com/lmweber/osta
• Owner: lmweber
• Created: 2020-06-08T16:07:01.000Z (almost 5 years ago)
• Default Branch: devel
• Last Pushed: 2025-02-01T15:27:11.000Z (4 months ago)
• Last Synced: 2025-02-01T16:28:01.587Z (4 months ago)
• Topics: analysis-workflows, bioconductor, spatial-transcriptomics, spatially-resolved-transcriptomics
• Language: TeX
• Homepage: https://lmweber.org/PrinciplesSTA/
• Size: 201 MB
• Stars: 54
• Watchers: 9
• Forks: 22
• Open Issues: 30
• Metadata Files:
  • Readme: README.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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README

        
# Orchestrating Spatial Transcriptomics Analysis with Bioconductor

[![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)  

[![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)

## Overview

This repository contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book.

## Link to book

The development version of the book is available at: https://lmweber.org/OSTA/

## 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, run the following in an R session in the `inst/` directory (after installing all dependencies):

```

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.

### Instructions

In each analysis / method chapter, we aim to include the following:

- brief background and overview

- mention any relevant benchmark papers

- demonstrate 1-2 key methods available in Bioconductor using code examples

- (optional) mention any other important methods in text (but keep concise)

Workflow chapters are longer and are intended to demonstrate a comprehensive workflow for a given data type / technological platform.

Please keep any added file sizes (e.g. images) as small as possible, and/or commit only code files.