Lecture and lab topics

Biological domains

  • RNA-Seq from sequences to analysis: mapping, quantification at gene and transcript level
  • Single cell (droplet based) RNA-seq: exploratory analysis, quality assessment
  • Mass spectrometry-based proteomics and metabolomics
  • Image-based data and spatial omics (CODEX, MERFISH et al.)
  • Emerging topics and participant suggestions

Statistics and data science

  • Introduction to the Bioconductor project (community, infrastructure, data structures, annotation resources)
  • Visualization, including interactivity, PCA and other low-dimensional embeddings, clustering, distances, nearest-neighbour graphs
  • Statistical hypothesis testing, false discovery rate, multiple testing, filtering and weighting
  • Regression: experimental design and design matrices, power, identifiability, diagnostics, generalized linear models
  • Classification / supervised machine learning, multi-omic data integration methods
  • Data manipulation, EDA, and tidy data analysis, applied to high dimensional biological data
  • Reproducibility, best practices for computational research, method comparison, benchmarking
  • Emerging topics and participant suggestions

Schedule (subject to change)

Date/Time Content
Sun 23 June
18:00-20:00 Registration & help desk
18:00-20:00 Get together with drinks
Mon 24 June
08:30-09:15 Lecture: Introduction to Bioconductor (Maria Doyle)
09:15-10:00 Lecture: Transcriptomics: biology of transcription, quantification, batch effects and QC (Michael Love)
10:00-10:30 ~~~ Coffee ~~~
10:30-11:15 Lecture: Regression: power, identifiability, diagnostics (Vince Carey)
11:15-12:00 Lecture: Statistical testing and multiple hypotheses (Wolfgang Huber) Further reading: book chapter
12:00-14:00 ~~~ Lunch break ~~~
14:00-17:00 Lab: R and Bioconductor basics
17:00-17:30 Intro to Project Groups: Creation of week-long project groups
20:10-22:00 Evening session: First meeting of the project groups, introductions
Tue 25 June
08:30-09:15 Lecture: RNA-Seq: Types of DE, modeling counts, scaling, transcript lengths, parameter estimation (Charlotte Soneson)
09:15-10:00 Lecture: Single-cell RNA-seq: exploration, quality control, low-dimensional embeddings (Davide Risso)
10:00-10:30 ~~~ Coffee ~~~
10:30-11:15 Lecture: Dimension reduction: PCA and other low-dimensional embeddings (Robert Gentleman)
11:15-12:00 Lecture: Distances, nearest-neighbour graphs and clustering (Vincent Carey)
12:00-14:00 ~~~ Lunch break ~~~
14:00-17:00 Lab: End-to-end RNA-Seq workflow
14:00-17:00 Lab: Single-cell transcriptomics
17:00-17:30 Flashlight talks
20:10-22:00 Evening session: Drinks will be provided
20:10-21:00 Group work: Continuation of projects from Monday night
21:00-22:00 Break-out discussions
Wed 26 June
08:30-09:15 Lecture: Chromatin accessibility and ATAC-seq (Michael Love) lab
09:15-10:00 Lecture: Single cell RNA-seq advanced topics: pseudo-bulking, double-dipping (Charlotte Soneson)
10:00-10:30 ~~~ Coffee ~~~
10:30-11:15 Lecture: Multi-condition single cell RNA-seq differential analysis (or when is the right time to categorize?) (Wolfgang Huber) Further reading: article
11:15-12:00 Lecture: Single cell advanced topics: multi-omics (Davide Risso)
12:00-14:00 ~~~ Lunch break ~~~
14:00-17:00 Social Programme: Excursion to the mountains and dinner Photos: By WH
Thu 27 June
08:30-09:30 Lecture: Mass spectrometry-based proteomics including single-cell (Laurent Gatto)
09:30-10:00 Lecture: Mass spectrometry-based metabolomics (Philippine Louail)
10:00-10:30 ~~~ Coffee ~~~
10:30-12:00 Lab: Proteomics/metabolomics (Laurent Gatto and Philippine Louail)
12:00-14:00 ~~~ Lunch break ~~~
14:00-14:45 Lecture: Spatial (transcript)omics (Davide Risso)
14:45-15:15 Lecture:: Bioconductor advanced topics: annotation resources (Vince Carey)
15:30-17:00 Lab: Multi-condition single cell RNA-seq differential analysis
15:30-17:00 Lab: Intro to Tidyomics: tidy data analysis applied to omics data
15:30-17:00 Lab: Spatial Transcriptomics
15:30-17:00 Lab: Trajectory analysis with slingshot and tradeSeq
15:30-17:00 Lab: Interactive exploration with iSEE
15:30-17:00 Lab: Working with Image Data
17:00-17:30 Flashlight talks
20:10-22:00 Evening session: Drinks will be provided
20:10-22:00 Group work: (on your own) Finalizing group work for presentations Friday afternoon
Fri 28 June
08:30-09:15 Lecture: Design of High Throughput Experiments and their Analysis (Charlotte Soneson)
09:15-10:00 Lecture: Machine learning (Robert Gentleman)
10:00-10:30 ~~~ Coffee ~~~
10:30-11:15 Lecture: The multiplicity of possible analysis strategies (and how to handle it) in omics applications (Anne-Laure Boulesteix)
11:15-12:00 Lecture: The multiplicity of possible analysis strategies (and how to handle it) in benchmark studies (Anne-Laure Boulesteix)
12:00 Closing remarks
12:15-14:00 ~~~ Lunch break ~~~
14:00-15:30 Group project presentations
15:30-16:00 ~~~ Coffee ~~~
16:00-16:30 Career panel discussion

Lecturers and Teaching Assistants

Anne-Laure Boulesteix (ALB) Vince Carey (VJC) Maria Doyle (MD) Laurent Gatto (LG) Robert Gentleman (RG) Wolfgang Huber (WH) Philippine Louail (PL) Michael Love (ML) Davide Risso (DR) Charlotte Soneson (CS) Ilaria Billato (IB)