Clustering & UMAP

Duration: 45 min

Lecture Material:

Outline

  • 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. 

References.

Amezquita R, Lun A, Hicks S, Gottardo R, O’Callaghan A. (2023). Orchestrating Single-Cell Analysis with Bioconductor. Bioconductor. https://bioconductor.org/books/release/OSCA/

Brennecke P, et. al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods. 2013 Nov;10(11):1093-5. doi: 10.1038/nmeth.2645. Epub 2013 Sep 22. Erratum in: Nat Methods. 2014 Feb;11(2):210. PMID: 24056876.

Lun AT, McCarthy DJ, Marioni JC. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 2016 Aug 31;5:2122. doi: 10.12688/f1000research.9501.2. PMID: 27909575; PMCID: PMC5112579.

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. https://doi.org/10.5281/zenodo.5826256

Satija Lab. (2023). Cell-Cycle Scoring and Regression. https://satijalab.org/seurat/articles/cell_cycle_vignette . Accessed: September 2023.

Satija Lab. (2023). Seurat - Guided Clustering Tutorial. https://satijalab.org/seurat/articles/pbmc3k_tutorial.html . Accessed: September 2023.

Shahsavari A, Munteanu A, Mohorianu I. (2022) ClustAssess: tools for assessing the robustness of single-cell clustering. bioRxiv 2022.01.31.478592; doi: https://doi.org/10.1101/2022.01.31.478592

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.

Zappia L, Phipson B, Oshlack A. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS Comput Biol. 2018 Jun 25;14(6):e1006245. doi: 10.1371/journal.pcbi.1006245. PMID: 29939984; PMCID: PMC6034903.