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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.