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The Oxford Biomedical Data Science Training Programme delivers training in the skills and methods required for the analysis and interpretation of large-scale biomedical datasets, particularly genomic and functional genomic data.

The OBDS programme was established in 2018 with funding from Wellcome, the Cancer Research UK Oxford Centre and the NIHR Oxford Biomedical Research Centre, following a successful pilot programme within the MRC Computational Genomics Analysis and Training programme. To date the programme has trained over 80 biomedical researchers, who have benefited from the course in different ways (see testimonials).

This unique programme runs three times per year, with timings aligned to the University of Oxford terms. Numbers are limited to 8 participants per cohort and application is through a competitive process. The programme delivers  face-to-face online lectures, tutorials and group exercises. Our multi-week format and small group size enable us to go step-by-step through real world scenarios from setting up software environments to processing data and visualisation of results. The interactive format encourages participants to lead group exercises; quickly building the confidence and resilience required for independent work.  

 

In September 2021, we will be piloting a shorter 4-week course focussing on Linux and R programming with an emphasis on single-cell RNAseq data analysis. This R/Single-cell course is open to all University of Oxford staff and D.Phil. students and costs £4000. 

Three scholarships per cohort have been generously funded by the Precision Medicine Cluster of the Oxford NIHR Biomedical Research Centre. Places will be awarded by a review committee based on the scientific quality of the proposed project and training needs of the individual. To be considered for a BRC scholarship, projects must fall within the remit of the NIHR, which funds research for patient benefit, and must focus on analysis of human samples. Priority will be given to applicants in research groups affiliated with one of the five themes of the BRC Precision Medicine Cluster, namely Multi-modal Cancer Therapies, Molecular Diagnostics, Genomic Medicine, Respiratory, and Haematology and Stem Cells. However, applications from all BRC Themes will be considered if there are sufficient spaces available. Details of all BRC Themes are available on the Oxford BRC website

The Cancer Research UK Oxford Centre offers two fully funded places per term. To be considered for CRUK funding,  research projects must be cancer research focused and applicants must be CRUK Oxford Centre members (you can sign up here). CRUK funding will be allocated by representatives of the Centre Management Group on the basis of both application quality and fit with Centre strategy (details of which can be found here).

 

 For more information please contact fiona.lambert@imm.ox.ac.uk

 

Download the September 2021 cohort <application form>

 

September 2021 Course content

Subject

Topics

Computer systems

  • Linux command line:
    • navigating file systems
    • managing Linux processes
    • manipulating text files
    • running bioinformatics tools
  • Managing your software environment using Conda
  • High Performance Computing using Slurm
  • Version control with Git and GitHub
  • Best practice in data management

R for Data Science

  • R syntax and data structures
  • Programmjng concepts in R
  • The RStudio IDE
  • Managing your R environment using Renv
  • Data visualisation with ggplot2
  • Data wrangling with Tidyverse

R for Statistics and Genomics

    • Probability distributions and statistical tests
    • Dimensionality reduction and clustering
    • Introduction to Bioconductor for Genomics in R
    • Differential gene expression using DESeq2
    • Pathway and gene set analysis

    R for single-cell RNAseq

    • Cite-seq analysis using Seurat
    • scRNAseq analysis using Bioconductor
    • Assessing doublets and background
    • Single-cell dataset integration
    • Trajectory analysis

     

     

    Upcoming Courses

    Cohort Applications Open Applications close Course starts Course Ends
    January 2021 closed closed

    18/01/2021

    11/03/2021
    May 2021 closed closed

    03/05/2021

    24/06/2021
    September 2021 21/06/2021 19/07/2021 5pm

    27/09/2021

    22/10/2021