# 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: 1.18.0
Modified: 2025-01-20
Compiled: 2025-11-03
Environment: R version 4.5.1 Patched (2025-08-23 r88802), Bioconductor 3.22
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.