Tutorial for scRNA-seq data analysis beginners in Python

Currently, this tutorial includes the following parts:

1. The basic and routine analysis on one scRNA-seq data set using Scanpy in Python;
2. The basic pseudotime, trajectory and fate probability analysis
3. Data integration or batch effect correction for joint analysis of multiple scRNA-seq data sets;

What will be coming next:

1. Brief introduction of more advanced analysis, including RNA velocity analysis and cell-cell communication analysis;
2. Deep-learning-based data integration and projection.

The tutorial is available in three different format: HTML (Tutorial.html), Markdown (Tutorial.md) and Jupyter notebook (Tutorial.ipynb).

The example data used in this tutorial are mostly from the paper Organoid single-cell genomic atlas uncovers human-specific features of brain development.

Please contact Dr. Zhisong He (zhisong.he(at)bsse.ethz.ch) if there is any question.