course_schedule.qmd

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

::: {.callout-note}
**Other than** the **starting time**, the time schedule is an **approximation**. Because we cannot plan a course by the minute, in practice the time points will deviate. 
:::

## Day 1

| block   	| start    	| end      	| subject                        	|
|---------	|----------	|----------	|--------------------------------	|
| introduction 	| 9:15 AM  	| 9:30 AM 	| [Introduction](ipynb/day1-1_setup.ipynb) |
| block 1 	| 9:30 AM  	| 10:15 AM 	| [Introduction scRNAseq](ipynb/day1-1_setup.ipynb) |
|         	| 10:15 AM 	| 10:45 AM 	| BREAK                          	|
| block 2 	| 10:45 AM 	| 12:00 PM 	| Presentation: Andreia Gouvêa, 10X Field Application Scientist 	     |
|         	| 12:00 PM 	| 1:00 PM  	| BREAK                          	|
| block 3 	| 1:00 PM  	| 3:00 PM  	| [Cell Ranger](ipynb/day1-1_cellranger.ipynb)             	 |
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                          	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [Quality Control](ipynb/day1-2_analysis_tools_qc.ipynb) and [Normalization and Scaling](ipynb/day1-3_normalization_scaling.ipynb)                  


## Day 2

| block   	| start    	| end      	| subject                             	|
|---------	|----------	|----------	|-------------------------------------	|
| block 1 	| 9:15 AM  	| 10:15 AM 	| [Normalization and Scaling](ipynb/day1-3_normalization_scaling.ipynb) 	|
|         	| 10:15 AM 	| 10:45 AM 	| BREAK                               	|
| block 2 	| 10:45 AM  	| 12:15 PM 	| [Dimensionality Reduction](ipynb/day2-1_dimensionality_reduction.ipynb) and [Integration](ipynb/day2-2_integration.ipynb)	|
|         	| 12:15 PM 	| 1:15 PM  	| BREAK                               	|
| block 3 	| 1:15 PM  	| 3:00 PM  	| [Clustering](ipynb/day2-3_clustering.ipynb) and [Visualization](ipynb/day2-4_visualization.ipynb)     	|
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                               	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [Visualization & Cell Annotation](ipynb/day2-4_visualization.ipynb) 	|

## Day 3

| block   	| start    	| end      	| subject                             	|
|---------	|----------	|----------	|-------------------------------------	|
| block 1 	| 9:15 AM  	| 10:30 AM 	| [Transcription factor analysis](ipynb/day3-1_tf.ipynb)	|
|         	| 10:30 AM 	| 11:00 AM 	| BREAK                               	|
| block 2 	| 11:00 AM 	| 12:30 PM 	| [Trajectory Inference](ipynb/day3-3_trajectory_analysis.ipynb)            	|
|         	| 12:30 PM 	| 1:30 PM  	| BREAK                               	|
| block 3 	| 1:30 PM  	| 3:00 PM  	| [RNA velocity](ipynb/day3-4_velocity1.ipynb)  |
|         	| 3:00 PM  	| 3:30 PM  	| BREAK                               	|
| block 4 	| 3:30 PM  	| 5:00 PM  	| [RNA velocity](ipynb/day3-4_velocity2.ipynb) 	|