Orchestrating Spatial Transcriptomics Analysis with Bioconductor

Published: March 12, 2025

Welcome

This is the website for the online book Orchestrating Spatial Transcriptomics Analysis with Bioconductor.

This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial omics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets. In a few cases, R code is integrated with Python tools.

The book is organized into several parts, consisting of introductory materials, and analysis steps and workflows for the two main streams of spatial omics data: sequencing-based and imaging-based.

Additional materials on analysis workflows for non-spatial single-cell data, as well as further introductory materials on R and Bioconductor, can be found in the related book Orchestrating Single-Cell Analysis with Bioconductor (OSCA).