https://github.com/lmweber/principlessta

"Principles of Spatial Transcriptomics Analysis with Bioconductor" book
https://github.com/lmweber/principlessta

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

Last synced: 14 days ago
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"Principles of Spatial Transcriptomics Analysis with Bioconductor" book

• Host: GitHub
• URL: https://github.com/lmweber/principlessta
• Owner: lmweber
• Created: 2020-06-08T16:07:01.000Z (over 4 years ago)
• Default Branch: devel
• Last Pushed: 2024-09-30T19:00:18.000Z (about 1 month ago)
• Last Synced: 2024-10-13T05:40:11.875Z (27 days ago)
• Topics: analysis-workflows, bioconductor, spatial-transcriptomics, spatially-resolved-transcriptomics
• Language: TeX
• Homepage: https://lmweber.org/PrinciplesSTA/
• Size: 220 MB
• Stars: 38
• Watchers: 10
• Forks: 9
• Open Issues: 9
• Metadata Files:
  • Readme: README.md

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README

        
# Principles of Spatial Transcriptomics Analysis with Bioconductor

📖 [Book](https://lmweber.github.io/PrinciplesSTA/devel) [![deployment](https://img.shields.io/github/actions/workflow/status/lmweber/PrinciplesSTA/pages/pages-build-deployment?label=Book%20deployment)](https://github.com/lmweber/PrinciplesSTA/actions/workflows/pages/pages-build-deployment)  

🐳 [Docker](https://github.com/lmweber/PrinciplesSTA/pkgs/container/PrinciplesSTA) [![biocbook](https://img.shields.io/github/actions/workflow/status/lmweber/PrinciplesSTA/biocbook.yml?label=Docker%20image)](https://github.com/lmweber/PrinciplesSTA/actions/workflows/biocbook.yml)

## Overview

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

## Link to book

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

## For developers: publish updated version of book

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")

```

## For developers: preview locally

To build and preview the book locally, use the following code:

```

library(BiocBook)

bb <- BiocBook(".")

preview(bb)

```

## For developers: image files

Image files are stored separately in the [PrinciplesSTA-resources](https://github.com/lmweber/PrinciplesSTA-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.

## BiocBook

This book is built using the [BiocBook](https://github.com/js2264/BiocBook) package, developed by [Jacques Serizay](https://jserizay.com/) for building Quarto books with Bioconductor. More details on BiocBook can be found in the [BiocBook book](https://jserizay.com/BiocBookDemo/devel/).