Hands On Session 3: single-cell data preparation and clustering

Duration: 60 min

Hands-on material:

  • Link to Drive

    • Data and scripts: HandsOn3_SingleCell_Data_QC/ folder

    • Script: hands-on-session3_data-preparation-and-clustering.Rmd

Outline:

  • Data loading and object creation:

    • SeuratObject

    • SingleCellExperiment

    • Converting between formats

  • Data visualization and exploratory analysis using Principal Component Analysis (PCA)

  • Quality control (QC):

    • Cell QC

    • Feature QC

  • Normalization and feature selection:

    • Normalization

    • Feature selection

  • Cell cycle scoring

  • Cell clustering