CUrriculum

Monday   9:30-17:30

 

     9:30    Lecture 0  General Introduction / Overview of the course
    10:00   Lecture 1  Introduction to GWAS: Linkage disequilibrium and Linear Regression
    11:00    coffee break
    11:15    Lecture 2  Introduction to GWAS: Linkage disequilibrium and Linear Regression
    12:00   Lecture 3  GWAS: case studies / examples from literature
                  Lab 2 - part 1    basic Linux and R
    13:00    lunch break
    14:00    Lab 2 - part 2    Practicalities and set-up (server, github repo, conda envs, etc) and description of datasets
    15:00    Lab 2 - part 3    basic Linux and R
    15:30    coffee break
    16:00    Lab 3    GWAS: basic models
    16:30    Lab 3 (demonstration)    GWAS: basic models (linear and logistic regression, population structure, etc.)
           
Tuesday    9:30-17:30

 

     9:30     Lecture 4    EDA: theory
    10:00    Lab 4    EDA practice
    11:00    coffee break
    11:15      Lecture 5    data preprocessing: theory
    12:00    Lab 5    data preprocessing: practice
    13:00    lunch break
    14:00    Lecture 6    Imputation of missing genotypes: theory
    15:00    Lab 6 - part 1    practical session on imputation (Beagle)
    15:30    coffee break
    16:00    Lab 6 - part 2    practical session on imputation (Beagle)
    16:30    Lab 7 (demonstration)    KNNI imputation
           
Wednesday    9:30-17:30

 

    09:30    Lecture 7    GWAS, the full model (all SNPs)
    11:00    coffee break
    11:15      Lab 9 (demonstration)  a few steps in the past (GenABEL)
    12:00    Lab 10   GWAS: the stand-alone script(s) for the full model
    13:00    lunch break
    14:00    Lecture 8 GWAS: experimental design and statistical power
    15:00    coffee break
    15:30    Lecture 9  The multiple testing issue?
    16:30    Lab 10  revising the steps involved in GWAS
           
Thursday    9:30-17:30

 

     9:30    Lecture 10    Bioinformatics pipelines: a super-elementary introduction
    10:30    Lab 11    Building a pipeline with Snakemake
    11:15    coffee break
    11:30    Lab 12    The GWAS pipeline for continuous phenotype
                  Lab 13    The GWAS pipeline for binary phenotype
    13:00    lunch break
    14:00    Lab 14    Introducing the assignment (+ light touch on RMarkdown)
    14:30    Assignment (groups)    Build your own GWAS pipeline on new data
    15:30    coffee break
    16:00    Assignment (groups)    Build your own GWAS pipeline on new data
           
Friday    9:30-17:30

 

     9:30  Assignment (groups)    Build your own GWAS pipeline on new data
    11:00    coffee break
    11:30    Assignment (groups)    Build your own GWAS pipeline on new data
    12:30    Assignment (groups)    Presenting and discussing results
    13:00    lunch break
    14:00    Assignment (groups)    Presenting and discussing results
    15:30    coffee break
    16:00    Lecture 11    A light touch on post-GWAS analysis
    17:00    Lecture 12    A glimpse on ROH-based alternative