Schedule

09:00 - 10:00 Introductory lecture (Vincent Gardeux)
10:00 - 11:00 Quantification, QC & Normalization (Davide Risso)
11:00 - 11:30 Coffee break
11:30 - 12:30 Dimensionality reduction (Paulo Czarnewski)
12:30 - 14:00 Lunch break
14:00 - 18:00 Hands-on + Coffee break (Davide, Paulo): Scater_QC (html) (Bioc 3.10), Scater_DR (html) | Seurat analysis pipeline: Seurat_qc, Seurat_DR
18:00 - 20:00 Free time / spa
20:00 Dinner

09:00 - 10:00 Batch correction (Panagiotis Papasaikas)
10:00 - 11:00 Clustering - methods overview (Charlotte Soneson)
11:00 - 11:30 Coffee break
11:30 - 12:30 Cell fate mapping and trajectories (Wouter Saelens)
12:30 - 14:00 Lunch break
14:00 - 18:00 Hands-on + Coffee break (Panagiotis, Charlotte, Wouter): Batch Correction (html) (Helper_Functions.R), Clustering (html), Trajectories and RNA velocity
18:00 - 20:00 Free time / spa
20:00 Special dinner - Cheese fondue

09:00 - 11.00 Differential expression, interactive visualization (Charlotte Soneson)
11.00 - 11.30 Coffee break
11.30 - 12.30 Hands-on: interactive visualization (html), differential expression (html), automatic cell type assignment html
12:30 - 14:00 Lunch break
14.00 - 18:00 Team activity (hiking)
18:30 - 19:30 Keynote lecture: Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuven, Belgium.
20:00 Dinner

09:00 - 10:30 Differential abundance (DA) and state (DS) analysis for single-cell cytometry data (Mark Robinson & Helena Crowell)
10:30 - 11:00 Coffee break
11:00 - 12:30 DA and DS cytometry Hands-on (Helena, Mark): setup.R, F1000 workflow (Rmd, html)
12:30 - 14:00 Lunch break
14:00 - 15:30 Transcriptome + proteome Transcriptome + proteome presentation (Johan Reimegård)
15:30 - 16:00 Coffee break
16:00 - 17:30 Transcriptome/proteome Hands-on Transcriptome + proteome lab(html)(Johan Reimegård)
18:45 Dinner
20:00 - 22:00 Special late opening of the spa

09:00 - 10:00 Technical overview of single-cell transcriptomics methods (Sebastien Smallwood)
10:00 - 11:00 Spatial mapping of scRNAseq (Lars Borm)
11:00 - 11:30 Coffee break
11:30 - 12:30 Lineage tracing and scRNA (Maria Florescu)
12:30 - 14:00 Lunch break
14:00 - 14:20 Conclusion and wrap up
14:20 End of the event
14:58 Train from Leysin-Feydey station