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 (Vince Carey) |
| 09:15-10:00 | Lecture: PCA and other low-dimensional embeddings (Robert Gentleman) |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-11:15 | Lecture: Regression: power, identifiability, diagnostics (Michael Love) |
| 11:15-12:00 | Lecture: Statistical testing and multiple hypotheses (Wolfgang Huber) |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-17:00 | Lab: R and Bioconductor basics |
| 17:00-17:30 | Flashlight talks |
| 20:10-22:00 | Evening session: Drinks will be provided |
| 20:30-21:30 | Group work: Creation of week-long project groups, choice of projects |
| Tue 25 June | |
| 08:30-09:15 | Lecture: RNA-seq intro: biology of transcription, quantification, batch effects and QC (Michael Love) |
| 09:15-10:00 | Lecture: RNA-Seq for DE: Types of DE, modeling counts, scaling, transcript lengths, parameter estimation (Charlotte Soneson) |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-11:15 | Lecture: Single-cell RNA-seq: exploration, quality control, low-dimensional embeddings (Davide Risso) |
| 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 |
| 20:30-21:30 | Group work: Continuation of projects from Monday night |
| Wed 26 June | |
| 08:30-09:15 | Lecture: Bioconductor advanced topics: annotation resources (Vince Carey) |
| 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) |
| 11:15-12:00 | Lecture: Single cell advanced topics: trajectories, multi-omics (Charlotte Soneson, Davide Risso) |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-17:00 | Social Programme: Excursion to the mountains and dinner |
| Thu 27 June | |
| 08:30-09:15 | Lecture: Mass spectrometry-based proteomics including single-cell (Laurent Gatto) |
| 09:15-10:00 | Lecture: Mass spectrometry-based metabolomics (Laurent Gatto) |
| 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:: R programming and debugging (Laurent Gatto) |
| 15:30-17:00 | Lab: Tidyomics project: tidy data analysis applied to omics data |
| 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 |
| 20:30-21:30 | Group work: 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) |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-17:00 | Group project presentations |
| 17:00 | Closing remarks |
Lecturers and Teaching Assistants
Anne-Laure Boulesteix (ALB) Vince Carey (VJC) Laurent Gatto (LG) Robert Gentleman (RG) Wolfgang Huber (WH) Michael Love (ML) Davide Risso (DR) Charlotte Soneson (CS) Ilaria Billato (IB) Philippine Louail (PL)