VI. Tutorial Single Cell Data Analysis

Macosko et al. dataset

Perform

• QC
• Feature selection
• Dimension reduction
• Clustering

on the Macosko dataset. A script with the steps can be found on Macosko.

The data can also be downloaded on the UFORA course website (content > scRNAseq Data).

Differential expression analysis

Follow chapter 4 of the OSCA book on multi-sample.

You can generate the input sce object using the OSCA book chapter or you can download it from the UFORA course website (content > scRNAseq Data).

Kang et al. dataset

1. Do the filtering and QC on the Kang dataset
2. Perform DE analysis for the stimulus effect in each cell type

Data can be loaded via

library(ExperimentHub)
eh <- ExperimentHub()
sce <- eh[["EH2259"]]

or on the UFORA course website (content > scRNAseq Data).