Single cell RNA-seq analysis workshop

Overview

This workshop is a shortened version of the SingleCellWorkshop from Yunshun Chen, and more details can be found here.

In this workshop, you will learn how to analyse single-cell RNA-seq count data using Seurat and ternary plot. This workshop uses one epithelium sample of human normal mammary gland, which can be obtained from the 10X Genomics dataset (GSE161529) of Pal et al. 2021. EMBO J.

Pre-requisites

The course is aimed at PhD students, Master’s students, and third & fourth year undergraduate students. Some basic R knowledge is assumed - this is not an introduction to R course. If you are not familiar with the R statistical programming language it is compulsory that you work through an introductory R course before you attend this workshop

R packages used

The following R packages will be used:

  • Seurat
  • edgeR
  • vcd
  • scales
  • pheatmap

Time outline

Activity Time
Introduction & setup 10m
Part 1. Standard analysis 35m
Part 2. Ternary plot analysis 05m
Q & A 10m

Workshop goals and objectives

Learning goals

  • Learn the standard scRNA-seq analysis pipeline.
  • Learn the ternary plot analysis for scRNA-seq data

Learning objectives

  • Perform standard analysis of a single 10X scRNA-seq sample.
  • Perform ternary plot analysis of a single 10X scRNA-seq sample

Workshop package installation

Guide

This is necessary in order to reproduce the code shown in the workshop. The workshop is designed for R 4.1 and can be installed using one of the two ways below.

Via Docker image

If you’re familiar with Docker you could use the Docker image which has all the software pre-configured to the correct versions.

docker run -e PASSWORD=abc -p 8787:8787 jinmingcheng/scrnaseqworkshop

Once running, navigate to http://localhost:8787/ and then login with Username:rstudio and Password:abc.

You should see the Rmarkdown file with all the workshop code which you can run.

Via GitHub

Alternatively, you could install the workshop using the commands below in R 4.1.

install.packages('remotes')

# Install workshop package
remotes::install_github("jinming-cheng/scRNAseqWorkshop", build_vignettes = TRUE)

# To view vignettes
library(scRNAseqWorkshop)
browseVignettes("scRNAseqWorkshop")