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Thu 23 May - Fri 24 May 2019
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Analysis of single cell RNA-seq data

Thu 23 May - Fri 24 May 2019


Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The course website providing links to the course materials can be found here.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
  • The course is intended for those who have basic familiarity with Unix and the R scripting language.
  • We will assume that you are familiar with mapping and analysing bulk RNA-seq data as well as with the commonly available tools used for this type of analysis.
  • We recommend either attending Introduction to R for Biologists, or working through the materials of the now discontinued An Introduction to Solving Biological Problems with R and the Introduction to RNA-seq data analysis before attending this course.
  • The course will be mostly beneficial to those who have, or will shortly have, scRNA-seq data ready to analyse.

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 23 May 2019   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Sebastian Mueller,  Maria Primo,  Tallulah Andrews,  Elo Madissoon,  Martin Hemberg,  Rocio T Martinez-Nunez
2 Fri 24 May 2019   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Tallulah Andrews,  Dr S. Ballereau,  Sebastian Mueller,  Maria Primo,  Elo Madissoon,  Jimmy Lee
Topics covered

Bioinformatics, Data handling, Data mining, Data visualisation, Functional genomics, Transcriptomics


After this course you should be able to:

  • Normalise scRNA-seq data
  • Visualise the data and apply dimensionality reduction
  • Use available tools for analysing differential expression
  • Use available methods for clustering
  • Use available methods for pseudo-time alignment

During this course you will learn about:

  • Normalization and correction for batch effects
  • Identification of differentially expressed genes
  • Unsupervised hard and soft clustering of cells

Presentation and demonstrations


Day 1 Topics
Session 1 Introduction to scRNA-seq
Session 2 Introduction to R/Bioconductor
Session 3 Construction of expression matrix
Session 4 Cleaning the expression matrix
Session 5 Normalization theory
Session 6 Normalization practice
Session 7 Dealing with confounders
Day 2
Session 1 Biological analysis
Session 2 Seurat
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



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