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Introduction to Single-cell RNA-seq Analysis

University of Cambridge / CRUK

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Introduction to single-cell RNA-seq data analysis

17, 24 June, 1 July 2022, 09:30 - 17:30

Bioinformatics Training Facility, 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.

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:

Schedule

Please not that we may adjust these times as the pace of the course requires.

Day 1

Day 2

Day 3