Single-cell and single-nuclei sequencing experiments reveal previously unseen molecular details. The number of sequencing procedures and computational data analysis approaches have been increasing rapidly in recent years. This chapter provides an overview of the current developments in single-cell analysis. An introduction and practical guidance for choosing the most suitable sequencing procedure to match individual experimental demands in the course of investigating biological hypotheses are presented. Basic data analysis approaches are highlighted, followed by a discussion on advanced downstream approaches to enrich the information obtained from single-cell experiments; for example, trajectory analysis, pseudotime assumptions, and network inference. Currently unsolved challenges are discussed to allow the reader to avoid the most common pitfalls.
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