Updated bioc compiled

NBISweden · Feb 5, 2024 · 96cd7ca · 96cd7ca
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commit 96cd7ca
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Showing 5 changed files with 5 additions and 7 deletions.
diff --git a/compiled/labs/bioc/bioc_02_dimred.qmd b/compiled/labs/bioc/bioc_02_dimred.qmd
@@ -31,7 +31,7 @@ suppressPackageStartupMessages({
 
 ``` {r}
 # download pre-computed data if missing or long compute
-fetch_data <- FALSE
+fetch_data <- TRUE
 
 # url for source and intermediate data
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"

diff --git a/compiled/labs/bioc/bioc_03_integration.qmd b/compiled/labs/bioc/bioc_03_integration.qmd
@@ -59,7 +59,7 @@ suppressPackageStartupMessages({
 
 ``` {r}
 # download pre-computed data if missing or long compute
-fetch_data <- FALSE
+fetch_data <- TRUE
 
 # url for source and intermediate data
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
@@ -261,7 +261,6 @@ Now we can run scanorama:
 ``` {r}
 #| fig-height: 5
 #| fig-width: 15
-#| eval: false
 
 scanorama <- reticulate::import("scanorama")
 
@@ -290,7 +289,6 @@ Now we will plot UMAPS with all three integration methods side by side.
 ``` {r}
 #| fig-height: 8
 #| fig-width: 10
-#| eval: false
 
 p1 <- plotReducedDim(sce, dimred = "UMAP_on_PCA", colour_by = "sample", point_size = 0.6) + ggplot2::ggtitle(label = "UMAP_on_PCA")
 p2 <- plotReducedDim(sce, dimred = "UMAP_on_MNN", colour_by = "sample", point_size = 0.6) + ggplot2::ggtitle(label = "UMAP_on_MNN")

diff --git a/compiled/labs/bioc/bioc_04_clustering.qmd b/compiled/labs/bioc/bioc_04_clustering.qmd
@@ -37,7 +37,7 @@ suppressPackageStartupMessages({
 
 ``` {r}
 # download pre-computed data if missing or long compute
-fetch_data <- FALSE
+fetch_data <- TRUE
 
 # url for source and intermediate data
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"

diff --git a/compiled/labs/bioc/bioc_05_dge.qmd b/compiled/labs/bioc/bioc_05_dge.qmd
@@ -40,7 +40,7 @@ suppressPackageStartupMessages({
 
 ``` {r}
 # download pre-computed data if missing or long compute
-fetch_data <- FALSE
+fetch_data <- TRUE
 
 # url for source and intermediate data
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"

diff --git a/compiled/labs/bioc/bioc_06_celltyping.qmd b/compiled/labs/bioc/bioc_06_celltyping.qmd
@@ -52,7 +52,7 @@ Let's read in the saved Covid-19 data object from the clustering step.
 
 ``` {r}
 # download pre-computed data if missing or long compute
-fetch_data <- FALSE
+fetch_data <- TRUE
 
 # url for source and intermediate data
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"