Single-cell RNA-seq introduction course

This course covers the basics of single-cell RNA-seq analysis. This material was meant to be continuously improved by the Dalmolin Systems Biology Group students.

This book is based on the following references:

• The experimental design of single-cell studies: Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
• Orchestrating Single-Cell Analysis with Bioconductor - Basics;
• Single-cell best practices
• Seurat cheatsheet
• Introduction to single-cell from Wellcome Connecting Science
• SingleR
• This awesome playlist on YouTube (in python): link

Install R packages:

Using conda or mamba

Note the environment.yml file. It has a list of R packages that are going to be used in this course. Install them by:

conda env create -f environment.yml

Activate the intro-single-cell environment:

conda activate intro-single-cell

Or using the install.R script

Please note the install.R script. In a R session, run

source("install.R")

Or run in the terminal:

Rscript install.R

Download the data

In your machine, download this folder and extract it to the same location of the course folder.

Datasets to practice

List of datasets to practice: link