Multi-Sample Single-Cell Analyses with Bioconductor

Authors: Robert Amezquita [aut], Aaron Lun [aut], Stephanie Hicks [aut], Raphael Gottardo [aut], Alan O’Callaghan [cre]
Version: 1.14.3
Modified: 2025-01-20
Compiled: 2025-01-22
Environment: R version 4.4.2 (2024-10-31), Bioconductor 3.20
License: CC BY
Copyright: Bioconductor, 2025
Source: https://github.com/OSCA-source/OSCA.multisample

Welcome

This site contains the advanced analysis chapters for the “Orchestrating Single-Cell Analysis with Bioconductor” book. This describes the handling of multiple samples in a single-cell RNA-seq analysis, starting with integration of multiple datasets into a common space for consistent analyses, differential expression comparisons between conditions based on pseudo-bulk samples, and differential abundance analyses for cell subpopulations. It is intended for readers who are already familiar with basic single-cell analyses, possibly after reading some of the prior books in this collection.