This workshop introduces the best practice bioinformatics methods for analyzing single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days which includes 4 days of lectures and exercises. Key topics covered: - Overview of the current scRNAseq technologies - Basic overview of pipelines for processing raw reads into expression values - Quality control and normalization - Dimensionality reduction techniques - Data integration and batch correction - Differential gene expression - Clustering techniques - Cell type prediction - Trajectory inference analysis - Comparison of Seurat, Bioconductor and Scanpy toolkits