Clustering & UMAP

Duration: 45 min

Lecture Material:


  • Introduction to scRNA-Seq Clustering

  • Previous steps

    • Normalization

    • Variable Feature Selection

    • Data correction

    • Dimensional Reduction

    • Integration

  • Clustering

    • Different algorithms

  • Visualization of the clustering

    • UMAP vs tSNE and why PCA is not suitable.

  • Clustering assessment. 


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Mary Piper, Meeta Mistry, Jihe Liu, William Gammerdinger, & Radhika Khetani. (2022, January 6). hbctraining/scRNA-seq_online: scRNA-seq Lessons from HCBC (first release). Zenodo.

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Satija Lab. (2023). Seurat - Guided Clustering Tutorial. . Accessed: September 2023.

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Stuart T, et. al. Comprehensive Integration of Single-Cell Data. Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6. PMID: 31178118; PMCID: PMC6687398.

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