Analysis of Single-Cell RNA-seq data in R

• January 30th University of Sheffield
• Bartolome House, Seminar Room EG03

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Overview

Recent advances in gene expression technologies have made it possible to measure transcription for individual cells - enabling researchers to understand cellular heterogeneity and understand complex tissue types. In this course we describe the analysis of data derived from such experiments using the R language.

We will focus specifically on data generated using the 10X protocol, although the methods will relevant to other technologies

Schedule (Provisonal)

Monday 30th January, 2023

• 09:30 - 11:00 Introduction and quality assessment
• 11:15 - 12:30 Normalisation and sources of variation
• 12:30 - 13:15 LUNCH
• 13:15 - 15:00 Clustering (UMAP, tSNE etc)
• 15:00 - 16:30 Identifying marker genes and differential expression

Materials

• Part 1 - Markdown
• Part 1 - HTML
• Part 2 - Markdown
• Part 2 - HTML
• Part 3 - Markdown
• Part 3 - HTML

Setup

1. First, install both R and RStudio for your operating system.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Mac

Install R by downloading and running this .pkg file from CRAN. Also, please install the free RStudio IDE

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install free the RStudio IDE.

2. Please download and extract (un-zip) this zip file into the directory on the computer that you wish to work in

• Course Data

3. Type the following into the R console to install some extra R packages required for the workshop

source("https://raw.githubusercontent.com/sheffield-bioinformatics-core/scrnaseq_course/main/install_packages.R")

Mac Users may get the following error message when trying to install these packages

xcrun error: inactive developer path (/Library/Developer/CommandLineTools), missing xcrun at:.....

If this is the case, you will need to follow the instructions from this link to install "Xcode"

https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a

Window users might get a message that Rtools is required. This shouldn't be necessary, but you might need it for other packages. It can be installed here:-

https://cran.r-project.org/bin/windows/Rtools/