---
title: "R packages for single-cell analysis"
canonical: "https://help.biobam.com/space/BTP/3342631013/R%20packages%20for%20single-cell%20analysis"
format: markdown
---
**Duration**: 30 min

**Lecture material**:

- [Slides PDF](https://drive.google.com/file/d/1URSRzGn8OmyEkbsXc16vjIXZTnQD0iqY/view?usp=drive_link)


**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:**

- [Advanced R: Object Oriented Programming](https://adv-r.hadley.nz/oo.html)
- [The Carpentries Incubator: S4 classes in Bioconductor](https://carpentries-incubator.github.io/bioc-project/05-s4.html)
- [Orchestrating Single-Cell Analysis: the SingleCellExperiment class](https://bioconductor.org/books/3.13/OSCA.intro/the-singlecellexperiment-class.html)