course_schedule.qmd

---
title: "Course schedule"
---

::: {.callout-note}
**Apart** from the **starting time** the time schedule is **indicative**. Because we can not plan a course by the minute, in practice the time points will deviate. 
:::

## Day 1

| block   	| start    	| end      	| subject                        	|
|---------	|----------	|----------	|--------------------------------	|
| introduction 	| 9:00 AM  	| 9:30 AM 	| [Introduction](day1/day1-1_setup.qmd) |
| block 1 	| 9:30 AM  	| 10:30 AM 	| [Introduction scRNAseq](day1/day1-1_setup.qmd) |
|         	| 10:30 AM 	| 11:00 AM 	| BREAK                          	|
| block 2 	| 11:00 AM 	| 12:30 PM 	| [Analysis tools and QC](day1/day1-2_analysis_tools_qc.qmd) 	     |
|         	| 12:30 PM 	| 1:30 PM  	| BREAK                          	|
| block 3 	| 1:30 PM  	| 3:00 PM  	| [Analysis tools and QC](day1/day1-2_analysis_tools_qc.qmd)             	 |
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                          	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [Normalization and scaling](day1/day1-3_normalization_scaling.qmd)                  |

## Day 2

| block   	| start    	| end      	| subject                             	|
|---------	|----------	|----------	|-------------------------------------	|
| block 1 	| 9:00 AM  	| 10:30 AM 	| [Integration](day2/day2-2_integration.qmd) and [Dimensionality reduction](day2/day2-1_dimensionality_reduction.qmd)	|
|         	| 10:30 AM 	| 11:00 AM 	| BREAK                               	|
| block 2 	| 11:00 AM 	| 12:30 PM 	| Further exercises  |
|         	| 12:30 PM 	| 1:30 PM  	| BREAK                               	|
| block 3 	| 1:30 PM  	| 3:00 PM  	| [Clustering](day2/day2-3_clustering.qmd)     	|
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                               	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [Cell annotation](day2/day2-4_cell_annotation.qmd) 	|

## Day 3

| block   	| start    	| end      	| subject                             	|
|---------	|----------	|----------	|-------------------------------------	|
| block 1 	| 9:00 AM  	| 10:30 AM 	| [Differential gene expression](day3/day3-1_differential_gene_expression.qmd)	|
|         	| 10:30 AM 	| 11:00 AM 	| BREAK                               	|
| block 2 	| 11:00 AM 	| 12:30 PM 	| [Enrichment analysis](day3/day3-2_enrichment_analysis.qmd)            	|
|         	| 12:30 PM 	| 1:30 PM  	| BREAK                               	|
| block 3 	| 1:30 PM  	| 3:00 PM  	| [Trajectory analysis](day3/day3-3_trajectory_analysis.qmd)  |
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                               	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [Advanced analyses](day3/day3-4_advanced_analyses.qmd) 	|