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This is the website for “Orchestrating Single-Cell Analysis with Bioconductor”, a book that teaches users some common workflows for the analysis of single-cell RNA-seq data (scRNA-seq). This book will teach you how to make use of cutting-edge Bioconductor tools to process, analyze, visualize, and explore scRNA-seq data. Additionally, it serves as an online companion for the manuscript “Orchestrating Single-Cell Analysis with Bioconductor”.

While we focus here on scRNA-seq data, a newer technology that profiles transcriptomes at the single-cell level, many of the tools, conventions, and analysis strategies utilized throughout this book are broadly applicable to other types of assays. By learning the grammar of Bioconductor workflows, we hope to provide you a starting point for the exploration of your own data, whether it be scRNA-seq or otherwise.

This book is organized into three parts. In the Preamble, we introduce the book and dive into resources for learning R and Bioconductor (both at a beginner and developer level). Part I ends with a tutorial for a key data infrastructure, the SingleCellExperiment class, that is used throughout Bioconductor for single-cell analysis and in the subsequent section.

The second part, Focus Topics, begins with an overview of the framework for analysis of scRNA-seq data, with deeper dives into specific topics are presented in each subsequent chapter.

THe third part, Workflows, provides primarily code detailing the analysis of various datasets throughout the book.

Finally, the Appendix highlights our contributors.

If you would like to cite this work, please use the reference “Orchestrating Single-Cell Analysis with Bioconductor”.


The book is written in RMarkdown with bookdown. OSCA is a collaborative effort, supported by various folks from the Bioconductor team who have contributed workflows, fixes, and improvements.

This website is free to use, and is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License.

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