Merge branch 'main' of https://github.com/sib-swiss/single-cell-pytho…

…n-training
sib-swiss · May 27, 2024 · ac24db7 · ac24db7
2 parents a086631 + 3be3ced
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diff --git a/Docker/requirements.txt b/Docker/requirements.txt
@@ -1,6 +1,6 @@
 scanpy
 pandas
-numpy
+numpy==1.23.4
 matplotlib
 seaborn
 harmonypy
@@ -14,3 +14,4 @@ velocycle
 doubletdetection==4.2
 celltypist==1.6.2
 pyscenic==0.12.1
+distributed==2023.12.1
diff --git a/_quarto.yml b/_quarto.yml
@@ -20,7 +20,7 @@ website:
       - href: course_schedule.qmd
       - text: "day 1"
         menu:
-          - href: "ipynb/day1-0_setup.ipynb"
+          - href: "ipynb/day1-1_setup.ipynb"
           - href: "ipynb/day1-1_cellranger.ipynb"
           - href: "ipynb/day1-2_analysis_tools_qc.ipynb"
           - href: "ipynb/day1-3_normalization_scaling.ipynb"

diff --git a/assets/pdf/03_cellranger.pdf b/assets/pdf/03_cellranger.pdf
diff --git a/assets/pdf/04_scanpy_workflow.pdf b/assets/pdf/04_scanpy_workflow.pdf
diff --git a/assets/pdf/08_clustering_day2.pdf b/assets/pdf/08_clustering_day2.pdf
diff --git a/assets/pdf/09_cell_type_annotation_and_visualization_day2.pdf b/assets/pdf/09_cell_type_annotation_and_visualization_day2.pdf
diff --git a/course_schedule.qmd b/course_schedule.qmd
@@ -11,7 +11,7 @@ title: "Course schedule"
 | 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/day1-0_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                          	|
@@ -24,7 +24,7 @@ title: "Course schedule"
 
 | block   	| start    	| end      	| subject                             	|
 |---------	|----------	|----------	|-------------------------------------	|
-| block 1 	| 9:15 AM  	| 10:30 AM 	| [Dimensionality Reduction](ipynb/day2-1_dimensionality_reduction.ipynb) and [Integration](ipynb/day2-2.integration.ipynb)	|
+| block 1 	| 9:15 AM  	| 10:30 AM 	| [Dimensionality Reduction](ipynb/day2-1_dimensionality_reduction.ipynb) and [Integration](ipynb/day2-2_integration.ipynb)	|
 |         	| 10:30 AM 	| 11:00 AM 	| BREAK                               	|
 | block 2 	| 11:00 AM 	| 12:30 PM 	| [Clustering](ipynb/day2-3_clustering.ipynb)  |
 |         	| 12:30 PM 	| 1:30 PM  	| BREAK                               	|
@@ -38,7 +38,7 @@ title: "Course schedule"
 |---------	|----------	|----------	|-------------------------------------	|
 | 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](day3/day3-3_trajectory_analysis.ipynb)            	|
+| 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                               	|

diff --git a/ipynb/Clustering_Marker_Genes_D2B2_Controls.ipynb b/ipynb/Clustering_Marker_Genes_D2B2_Controls.ipynb
diff --git a/ipynb/Dimensionality_Reduction_Embedding_D2B1_Controls.ipynb b/ipynb/Dimensionality_Reduction_Embedding_D2B1_Controls.ipynb
diff --git a/ipynb/Integration_D2B1_Controls.ipynb b/ipynb/Integration_D2B1_Controls.ipynb
diff --git a/ipynb/Normalization_And_Scaling_D1B3_Controls.ipynb b/ipynb/Normalization_And_Scaling_D1B3_Controls.ipynb