Merge pull request #23 from dcgc-bfx/update_ks9

Updated presentation slides

Author: andpet0101

docs/Seurat_Vignettes.png

@@ -26,25 +26,25 @@ execute:
 
 ## Schedule Overview
 
-Today, 20.01.2026  
-11:00 - 12:00 - Set up your computers  
-12:00 - 13:00 - Lunch Break  
-13:00 - 14:30 - Loading Xenium data into `R` and `Seurat`  
-14:30 - 14:50 - Coffee Break  
-14:50 - 15:00 - Group Photo  
-15:00 - 17:00 - Spatial Transcriptomics Data Analysis  
+Today, 20.01.2026 \
+11:00 - 12:00 - Set up your computers \
+12:00 - 13:00 - Lunch Break \
+13:00 - 14:30 - Loading Xenium data into `R` and `Seurat` \
+14:30 - 14:50 - Coffee Break \
+14:50 - 15:00 - Group Photo \
+15:00 - 17:00 - Spatial Transcriptomics Data Analysis \
 
  
 
-Tomorrow, 21.01.2026  
-09:00 - 10:20 - Continuation Data Analysis  
-10:20 - 10:40 - Coffee Break  
-10:40 - 12:00 - Continuation Data Analysis  
+Tomorrow, 21.01.2026 \
+09:00 - 10:20 - Continuation Data Analysis \
+10:20 - 10:40 - Coffee Break \
+10:40 - 12:00 - Continuation Data Analysis \
 
 ## Code Availability
 
-After the training, you will be able to access all materials via our GitHub repository: 
-https://github.com/dcgc-bfx/spatial-analysis-xenium-training
+After the training, you will be able to access all materials via our GitHub repository: \
+<https://github.com/dcgc-bfx/spatial-analysis-xenium-training>
 
 :::: {.columns}
 
@@ -62,7 +62,7 @@ You are welcome to contribute and develop the code further!
 
 ## Netiquette
 
-We prepared code - let us run it in sync with each other  
+We prepared code - let us run it in sync with each other \
 (do not run your code ahead of the trainer)
 
 &nbsp;
@@ -71,24 +71,88 @@ Ask questions - we are here to help you!
 
 ## LinkedIn
 
-Follow us on LinkedIn for updates on future trainings and events!   
-https://www.linkedin.com/company/dresden-concept-genome-center/   
+Follow us on LinkedIn for updates on future trainings and events! \
+<https://www.linkedin.com/company/dresden-concept-genome-center/>   
 ![](../docs/DcGC_LinkedIn.png){width=80%}
 
 &nbsp;
 
-https://www.linkedin.com/in/katrinsameith/   
-https://www.linkedin.com/in/ulrike-anne-friedrich-7940ab142/   
-https://www.linkedin.com/in/rajinder-gupta-11512751/   
+<https://www.linkedin.com/in/katrinsameith/> \
+<https://www.linkedin.com/in/ulrike-anne-friedrich-7940ab142/> \
+<https://www.linkedin.com/in/rajinder-gupta-11512751/> \
 
 ## Data Analysis Cafe
 
-Feel free to reach out to us for follow-up questions, and make use of our monthly Data Analysis Cafe:  
+Feel free to reach out to us for follow-up questions, and make use of our monthly Data Analysis Cafe: \
 ![](../docs/DcGC_DataAnalysisCafe_lowres.png){width=35%}
 
-## Spatial Analysis Flowchart
+## Literature and toolkits to get started 
+
+Best practices: \
+  - Single-cell best practices: <https://www.sc-best-practices.org/preamble.html> \
+
+&nbsp;
+
+Seurat: \
+  - Seurat Xenium Analysis Vignette: <https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2> \
+
+&nbsp;
+
+Alternatives to Seurat \
+  - Squidpy: <https://squidpy.readthedocs.io/en/stable/> \
+  - Giotto: <https://giottosuite.readthedocs.io/en/latest/> \
+  
+## Seurat vignettes are a good way to get started
+
+![](../docs/Seurat_Vignettes.png) 
+
+## Spatial Analysis Overview
 
 ![](../docs/SpatialAnalysisFlowchart.png) 
 
+## Clean-up
+
+- If you would like to keep your copies of the workbook material: \
+  - Please copy it now \
+  - The files are in your home directory on the HPC cluster \
+  - Do not copy the dataset files in the `datasets` directory. Instead, copy only the `download.R` file and use it for download \
+  
+&nbsp;
+
+- RStudio server jobs will be stopped automatically
+
+## How to use the code later on
+
+All workshop material is available online at: \
+<https://github.com/dcgc-bfx/spatial-analysis-xenium-training>
+
+&nbsp;
 
+On a linux machine, you can use our singularity container
+
+```
+# Command to download the singularity container
+singularity pull oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.6.6
+```
+
+&nbsp;
+
+On Windows or MacOS, you can install R and RStudio locally and install the required packages
+
+## LinkedIn
+
+Follow us on LinkedIn for updates on future trainings and events! \   
+<https://www.linkedin.com/company/dresden-concept-genome-center/>   
+![](../docs/DcGC_LinkedIn.png){width=80%}
+
+&nbsp;
+
+<https://www.linkedin.com/in/katrinsameith/> \
+<https://www.linkedin.com/in/ulrike-anne-friedrich-7940ab142/> \
+<https://www.linkedin.com/in/rajinder-gupta-11512751/> \
+
+## Data Analysis Cafe
+
+Feel free to reach out to us for follow-up questions, and make use of our monthly Data Analysis Cafe: \
+![](../docs/DcGC_DataAnalysisCafe_lowres.png){width=35%}