Tutorial for scRNA-seq data analysis beginners using R

This tutorial includes three different parts:

1. The most basic and routine analysis on one scRNA-seq data set using Seurat in R;
2. Data integration or batch effect correction for joint analysis of multiple scRNA-seq data sets;
3. Cell type annotation label transfer given the reference data set;
4. Brief introduction of more advanced analysis, including velocity analysis and ligand-receptor-pairing-based cell-cell communication analysis.

The example data used in this tutorial are mostly from the paper Organoid single-cell genomic atlas uncovers human-specific features of brain development. In addition, a subset of data presented in the paper Charting human development using a multi-endodermal organ atlas and organoid models is also included as the example data set for ligand-receptor pairing analysis.

Please contact Dr. Zhisong He (zhisong.he(at)bsse.ethz.ch) or Prof. Barbara Treutlein (barbara.treutlein(at)bsse.ethz.ch) if there is any question.