Curriculum

             Day 1: Introduction to statistical reasoning, GSEA and R (9:30-17:30)

 

            Lecture: "So you have a list of thousand gene names: why do we do HT analyses?"

 

 

            Hands-on guide: data preparation for gene set enrichment analysis

 

 

            Guided self-study: using R for data loading and basic statistical calculations

 

 

            Individual project work: loading data for the individual project

 

 

            Lecture: "Statistics gone wrong: basics of statistical problems in HT applications"

 

 

 

             Day 2: A functional analysis primer (9:30-17:30)

 

            Lecture: "Methods of pathway and functional analysis in gene set enrichment analyses"

 

 

            Hands-on guide: gene set enrichment techniques in R and other frameworks

 

 

            Guided self-study: comparing results of different gene set enrichment techniques

 

 

            Individual project work: biological interpretation of the results

 

 

            Lecture: "Common mistakes in functional analysis of HT data"

 

 

 

             Day 3: Getting the gene sets, building your own modules (9:30-17:30)

 

            Lecture: "Gene expression, co-expression and correlations"

 

 

            Hands-on guide: making your own modules

 

 

            Guided self-study: gathering gene sets for GSEA

 

 

            Individual project work

 

 

 

             Day 4: Beyond simple GSEA (9:30-17:30)

 

            Lecture: "Introduction to multivariate approaches and ML techniques"

 

 

            Hands-on guide: Practical guide to multivariate and ML techniques in R

 

 

            Hands-on guide: Using GSEA in single cell RNASeq

 

 

            Individual project work

 

 

            Lecture: "How to know when you are done?"

 

 

 

             Day 5: Evaluation of individual project (9:30-17:30)

 

            Guided self-study: problems from your research

 

 

            Individual work

 

 

            Student's presentations

 

 

            Discussion round

 

 

            Lecture: "Course wrap-up: where to go from here?"