UnivCambridge_ScRnaSeq_Nov2021

Introduction to single-cell RNA-seq data analysis

4th, 11th and 18th Nov 2021

Taught remotely

Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge

Instructors

Helpers:

Outline

This workshop is aimed at biologists interested in learning how to perform standard single-cell RNA-seq analyses.

This will focus on the droplet-based assay by 10X genomics and include running the accompanying cellranger pipeline to align reads to a genome reference and count the number of read per gene, reading the count data into R, quality control, normalisation, data set integration, clustering and identification of cluster marker genes, as well as differential expression and abundance analyses. You will also learn how to generate common plots for analysis and visualisation of gene expression data, such as TSNE, UMAP and violin plots.

We have run this course twice and are still learning how to teach it remotely. Please bear with us if there are any technical hitches, and be aware that timings for different sections laid out in the schedule below may not be adhered to. There may be some necessity to make adjusments to the course as we go.

(Materials linked to below will be updated closer to the time of delivery)

Prerequisites

**Some basic experience of using a UNIX/LINUX command line is assumed**

**Some R knowledge is assumed and essential. Without it, you will struggle on this course.** If you are not familiar with the R statistical programming language we strongly encourage you to work through an introductory R course before attempting these materials. We recommend our Introduction to R course

Data sets

Two data sets:

Tentative schedule

Tentative schedule for a 3-day course.

(long sessions include breaks)

Day 1: Thursday 4th Nov

Day 2: Thursday 11th Nov

Day 3: Thursday 18th Nov