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 6 July | |
| 18:00-20:00 | Registration & help desk |
| 18:00-20:00 | Get together with drinks |
| Mon 7 July | |
| 08:30-09:15 | Lecture: Introduction to Bioconductor |
| 09:15-10:00 | Lecture: Transcriptomics: biology of transcription, quantification, batch effects and QC |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-11:15 | Lecture: Regression: power, identifiability, diagnostics |
| 11:15-12:00 | Lecture: Statistical testing and multiple hypotheses |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-15:30 | Lab: R and Bioconductor basics |
| 15:30-16:00 | ~~~ Coffee ~~~ |
| 16:00-17:00 | Lab continuation |
| 17:00-17:30 | Intro to Project Groups (optional) |
| 20:10-22:00 | Evening session: Project groups and discussions |
| Tue 8 July | |
| 08:30-09:15 | Lecture: RNA-Seq differential expression |
| 09:15-10:00 | Lecture: Single-cell RNA-seq: exploration, quality control, low-dimensional embeddings |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-11:15 | Lecture: Dimension reduction: PCA and other low-dimensional embeddings |
| 11:15-12:00 | Lecture: Distances, nearest-neighbour graphs and clustering |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-15:30 | Lab: End-to-end RNA-Seq workflow |
| 14:00-15:30 | Lab: Single-cell transcriptomics |
| 15:30-16:00 | ~~~ Coffee ~~~ |
| 16:00-17:00 | Lab continuation |
| 17:00-17:30 | Flashlight talks |
| 20:10-22:00 | Evening session: Drinks will be provided |
| Wed 9 July | |
| 08:30-09:15 | Lecture: Chromatin accessibility and ATAC-seq |
| 09:15-10:00 | Lecture: Single cell RNA-seq advanced topics: pseudo-bulking, double-dipping |
| 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?) |
| 11:15-12:00 | Lecture: Single cell advanced topics: multi-omics |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-17:00 | Social Programme: Excursion to the mountains and dinner Photos: By WH |
| Thu 10 July | |
| 08:30-09:15 | Lecture: Mass spectrometry-based proteomics including single-cell |
| 09:15-10:00 | Lecture: Mass spectrometry-based metabolomics |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-12:00 | Lab: Proteomics |
| 10:30-12:00 | Lab: Metabolomics |
| 12:00-14:00 | ~~~ Lunch break ~~~ |
| 14:00-14:45 | Lecture: Spatial (transcript)omics |
| 14:45-15:15 | Lecture:: Bioconductor advanced topics: annotation resources |
| 15:15-15:30 | ~~~ Coffee ~~~ |
| 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 |
| 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 |
| Fri 11 July | |
| 08:30-09:15 | Lecture: Design of High Throughput Experiments and their Analysis |
| 09:15-10:00 | Lecture: Machine learning (Robert Gentleman) |
| 10:00-10:30 | ~~~ Coffee ~~~ |
| 10:30-11:15 | Lecture: AI tools for biology |
| 11:15-12:00 | Lecture: AI tools for biology |
| 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 |