Merge branch 'gh-pages' of github.com:dmgatti/SingleCellRNAseq into g…

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dmgatti · Oct 17, 2024 · 27e44b0 · 27e44b0
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diff --git a/_episodes/03-Overview-scRNA-seq-Data.md b/_episodes/03-Overview-scRNA-seq-Data.md
diff --git a/_episodes/04-Quality-Control.md b/_episodes/04-Quality-Control.md
diff --git a/_episodes/05-Common-Analyses.md b/_episodes/05-Common-Analyses.md
diff --git a/_episodes/06-Biology-Driven-Analyses.md b/_episodes/06-Biology-Driven-Analyses.md
@@ -306,28 +306,28 @@ Computing SNN
 
 
 ~~~
-17:28:15 UMAP embedding parameters a = 0.9922 b = 1.112
+02:26:05 UMAP embedding parameters a = 0.9922 b = 1.112
 ~~~
 {: .output}
 
 
 
 ~~~
-17:28:15 Read 44253 rows and found 24 numeric columns
+02:26:05 Read 44253 rows and found 24 numeric columns
 ~~~
 {: .output}
 
 
 
 ~~~
-17:28:15 Using Annoy for neighbor search, n_neighbors = 30
+02:26:05 Using Annoy for neighbor search, n_neighbors = 30
 ~~~
 {: .output}
 
 
 
 ~~~
-17:28:15 Building Annoy index with metric = cosine, n_trees = 50
+02:26:05 Building Annoy index with metric = cosine, n_trees = 50
 ~~~
 {: .output}
 
@@ -349,13 +349,13 @@ Computing SNN
 
 ~~~
 **************************************************|
-17:28:20 Writing NN index file to temp file C:\Users\c-dgatti\AppData\Local\Temp\Rtmp0etH6m\file1d103ffd4bf3
-17:28:20 Searching Annoy index using 1 thread, search_k = 3000
-17:28:32 Annoy recall = 100%
-17:28:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
-17:28:36 Initializing from normalized Laplacian + noise (using RSpectra)
-17:28:47 Commencing optimization for 200 epochs, with 1888044 positive edges
-17:29:31 Optimization finished
+02:26:09 Writing NN index file to temp file C:\Users\c-dgatti\AppData\Local\Temp\Rtmpua4Qd7\file2e34780d10a1
+02:26:09 Searching Annoy index using 1 thread, search_k = 3000
+02:26:20 Annoy recall = 100%
+02:26:21 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
+02:26:24 Initializing from normalized Laplacian + noise (using RSpectra)
+02:26:34 Commencing optimization for 200 epochs, with 1888044 positive edges
+02:27:12 Optimization finished
 ~~~
 {: .output}
 

diff --git a/_episodes_rmd/04-Quality-Control.Rmd b/_episodes_rmd/04-Quality-Control.Rmd
@@ -26,13 +26,17 @@ suppressPackageStartupMessages(library(Matrix))
 suppressPackageStartupMessages(library(SingleCellExperiment))
 suppressPackageStartupMessages(library(scds))
 suppressPackageStartupMessages(library(Seurat))
+data_dir <- '../data'
+```
+
+```{r test_chunk}
+dir(data_dir)
 ```
 
 
 ```{r load_data,include=FALSE}
 # Only needed to build lessons.
 # Don't use in course.
-data_dir <- '../data'
 load(file.path(data_dir, 'lesson03.Rdata'))
 ```
 

diff --git a/fig/rmd-03-cell_counts-1.png b/fig/rmd-03-cell_counts-1.png
diff --git a/fig/rmd-03-cell_counts-2.png b/fig/rmd-03-cell_counts-2.png
diff --git a/fig/rmd-03-counts_image-1.png b/fig/rmd-03-counts_image-1.png
diff --git a/fig/rmd-04-doublet_plot-1.png b/fig/rmd-04-doublet_plot-1.png
diff --git a/fig/rmd-04-filter_gene_counts-1.png b/fig/rmd-04-filter_gene_counts-1.png
diff --git a/fig/rmd-04-filter_gene_counts_5k-1.png b/fig/rmd-04-filter_gene_counts_5k-1.png
diff --git a/fig/rmd-04-filter_umi-1.png b/fig/rmd-04-filter_umi-1.png
diff --git a/fig/rmd-04-gene_count_hist_2-1.png b/fig/rmd-04-gene_count_hist_2-1.png
diff --git a/fig/rmd-04-genes_umi-1.png b/fig/rmd-04-genes_umi-1.png
diff --git a/fig/rmd-04-seurat_counts_plots-1.png b/fig/rmd-04-seurat_counts_plots-1.png
diff --git a/fig/rmd-04-seurat_counts_plots2-1.png b/fig/rmd-04-seurat_counts_plots2-1.png
diff --git a/fig/rmd-04-sum_cell_counts-1.png b/fig/rmd-04-sum_cell_counts-1.png
diff --git a/fig/rmd-05-elbow-1.png b/fig/rmd-05-elbow-1.png
diff --git a/fig/rmd-05-elbow2-1.png b/fig/rmd-05-elbow2-1.png
diff --git a/fig/rmd-05-elbow3-1.png b/fig/rmd-05-elbow3-1.png
diff --git a/fig/rmd-05-pcplot-1.png b/fig/rmd-05-pcplot-1.png
diff --git a/fig/rmd-05-plot_umap-1.png b/fig/rmd-05-plot_umap-1.png
diff --git a/fig/rmd-05-unnamed-chunk-2-1.png b/fig/rmd-05-unnamed-chunk-2-1.png
diff --git a/fig/rmd-05-var_features-1.png b/fig/rmd-05-var_features-1.png