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Thu 18 May, Fri 19 May, Mon 22 May 2023
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


Bookings cannot be made on this event (Event is completed).

Other dates:

Thu 16 May 2024

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Register your interest - if you cannot make any of the currently scheduled dates and would be interested in additional dates being scheduled.

Booking / availability

Analysis of single cell RNA-seq data (IN PERSON)

Thu 18 May, Fri 19 May, Mon 22 May 2023


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 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 or register your interest 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.
  • After you have booked a place, if you are unable to attend any of the live sessions and would like to work in your own time, please email the Bioinfo Team as Attendance will be taken on all courses. A charge is applied for non-attendance, including for registered university students.
  • Further details regarding eligibility criteria are available here
  • Highly Recommended: Basic familiarity with the Unix command line and the R scripting language. Please make sure to attend one of our courses on these topics (see related courses below). Otherwise, please work through these materials before attending this workshop: Basic Command Line and Introduction to R for biologists
  • Recommended: It will also be beneficial if you have some familiarity with the Analysis of bulk RNA-seq data. You can attend our course on this topic either before or after attending this course (link below).

Number of sessions: 3

# Date Time Venue Trainers
1 Thu 18 May 2023   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ashley Sawle,  Abigail Edwards,  Jon Price,  Roderik Kortlever,  Katarzyna Kania,  Hugo Tavares
2 Fri 19 May 2023   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ashley Sawle,  Dr A.J. Reid
3 Mon 22 May 2023   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Dr A.J. Reid,  Abigail Edwards
Topics covered

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


After this course you should be able to:

  • Know about different single-cell sequencing technologies available nowadays, their pros and cons and which you may want to use for your experiments
  • Process raw single-cell sequencing data and assess the quality of your data
  • Normalise scRNA-seq data
  • Visualise the data and apply dimensionality reduction
  • Apply methods for batch correction and data integration
  • Identify groups of similar cells by clustering and identify marker genes to differentiate them
  • Apply differential expression between conditions

During this course you will learn about:

  • Different scRNA-seq technologies and what kind of data you obtain from each
  • Processing raw sequencing data from the commonly-used 10x Chromium platform using cellranger and the Loupe browser for exploratory analysis of the data. Preparing reference genomes for mapping with cellranger.
  • Use several R/Bioconductor packages for downstream analysis of scRNA-seq data, including: data normalization, correction for batch effects, dimensionality reduction methods (PCA, t-SNE and UMAP), cell clustering and differential expression analysis.

Presentation and demonstrations


Day 1 Topics
Session 1 Introduction to scRNA-seq
Session 2 Alignment and construction of feature-barcode counts matrix from 10x Chromium data using cellranger. Exploratory analysis of cellranger output using the Loupe browser. Preparing reference genomes for cellranger.
Session 3 Introduction to scRNA-seq analysis in R/Bioconductor - QC and exploratory analysis.
Day 2 Topics
Session 1 Data normalisation
Session 2 Feature selection and dimensionality reduction
Session 3 Batch correction and data integration
Day 3 Topics
Session 1 Cell clustering
Session 2 Identification of cluster marker genes
Session 3 Differential expression between conditions
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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