Analysis and Visualization of Single-Cell Sequencing Data with Scanpy and MetaCell: A Tutorial

Methods Mol Biol. 2024:2757:383-445. doi: 10.1007/978-1-0716-3642-8_17.


The emergence and development of single-cell RNA sequencing (scRNA-seq) techniques enable researchers to perform large-scale analysis of the transcriptomic profiling at cell-specific resolution. Unsupervised clustering of scRNA-seq data is central for most studies, which is essential to identify novel cell types and their gene expression logics. Although an increasing number of algorithms and tools are available for scRNA-seq analysis, a practical guide for users to navigate the landscape remains underrepresented. This chapter presents an overview of the scRNA-seq data analysis pipeline, quality control, batch effect correction, data standardization, cell clustering and visualization, cluster correlation analysis, and marker gene identification. Taking the two broadly used analysis packages, i.e., Scanpy and MetaCell, as examples, we provide a hands-on guideline and comparison regarding the best practices for the above essential analysis steps and data visualization. Additionally, we compare both packages and algorithms using a scRNA-seq dataset of the ctenophore Mnemiopsis leidyi, which is representative of one of the earliest animal lineages, critical to understanding the origin and evolution of animal novelties. This pipeline can also be helpful for analyses of other taxa, especially prebilaterian animals, where these tools are under development (e.g., placozoan and Porifera).

Keywords: Batch effect correction; Cell types; Cell-type evolution; Dimension reduction; Marker gene selection; Mnemiopsis; Placozoa; Porifera; Single-cell clustering; Single-cell transcriptomics; Trichoplax; Ctenophora.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Cluster Analysis
  • Computational Biology / methods
  • Gene Expression Profiling* / methods
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis* / methods
  • Software*
  • Transcriptome / genetics