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)