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Course Aim

Recent developments in technology have enabled the exploration of complex biological systems at the single cell level, leading to new insights in the way the immune system is regulated in conditions such as cancer or auto-immune disorders. One of these technologies, mass cytometry, is now being applied in the context of clinical trials as a way to gain insights into the mechanism of action of treatments, as well as to unravel determinants of patient response. These new applications pose significant challenges for data analysis, and in this workshop employing interactive tutorials we will cover issues such as quality control, batch correction and single cell differential analysis, and the computational solutions that have been developed to address them.

By the end of this workshop participants will be capable of generating their own analytical pipeline for single-cell analysis.

Course Format

This course will take place as a workshop with presentations interspersed with interactive sessions.

Laptops required.

Short introduction to R basics encouraged before coming to workshop (links will be sent to participants before workshop); however interactive sessions will be designed to enable participation with basic understanding.

Attendees will need R software and Rstudio interface installed, and have Eduroam account for internet access.

https://www.r-project.org/
https://www.rstudio.com/products/RStudio/ http://help.it.ox.ac.uk/network/wireless/services/eduroam/index

Basic R programming skills, and a knowledge of cytometry or single-cell analysis are essential. Contact course coordinator for more details (sheila.mccartan@ndorms.ox.ac.uk

Course content

  1. Introduction to Cytometry tools in R – OpenCyto and FlowWorkspace
  2. Loading data - Pre-exisiting workspaces and creating an analysis from scratch
  3. Quality control - Sample-level similarity and Marker Enrichment Modelling
  4. Population identification – Clustering and Manual gating
  5. Differential analysis
  6. High dimensional data exploration with t-SNE, Radviz & Fan plots
  7. Wrapping it all together - Notebooks, scripts and pipelines

Course length

Total course length is 3 hours.

Participant numbers

24

Booking Instructions

Please read the updated instructions before booking. 

Terms and Conditions

Please read the Terms and Conditions for course booking and attendance. These have been updated for Trinity Term 2019.

*** NEW COURSES ***

Understanding Intellectual Property (IP) workshop, 6 June. Open to all University students, researchers and staff. Provided by Research Services, Oxford University Innovation and the Careers Service.

'Academic English' courses available at the Oxford University Language Centre to help international students and staff improve their academic communication.

Limited spaces available for non-RDM MSD research staff on the RDM Learning and Development programme

iSkills for the Medical Sciences Division: Introduction to Mendeley (run by Bodleian iSkills) - book now for places during April-July.

Mixing it up mixed research methods course at the Department for Continuing Education (free for Oxford DPhil students) - 23 April to 11 June

Writing a medical conference abstract 11 June

How and why to undertake a systematic review 21 June 

Forthcoming events

Scientific Computing in MATLAB

Wednesday, 08 May 2019 to Wednesday, 19 June 2019, 9am - 5pm

This course is scheduled in Trinity term.

Introduction to statistics (Group B)

Monday, 17 June 2019, 1pm to 4pm

This course is scheduled in Michaelmas and Hilary term. Due to the high demand two more session were added in Trinity term.

Transfer of Status

Thursday, 20 June 2019, 2pm to 5pm

COURSE FULL This course is scheduled each term.

How and why to undertake a systematic review

Friday, 21 June 2019, 2pm to 4.30pm

This is a new course scheduled this term.

Experimental Design: the Good, the Bad and the Ugly

Wednesday, 26 June 2019, 9am to 5pm

This course is scheduled each term.