R packages for single-cell analysis

Duration: 30 min

Lecture material:

Lecture outline:

  • Introduction: R programming language, R Studio and Bioconductor

  • Relevant R packages for single-cell analysis:

    • Seurat environment

    • QC/normalization: scater, scran

    • Clustering: Seurat, OSCA

    • Cell type annotation: AUCell, SingleR

    • Differential abundance testing: milo

    • Pseudotime: Monocle

  • Single-cell R landscape:

    • S4 objects in R

    • SeuratObject class

    • SingleCellExperiment class

References: