diff --git a/rmd/30_BatchEffects.Rmd b/rmd/30_BatchEffects.Rmd index 7f3113b..86c3efe 100644 --- a/rmd/30_BatchEffects.Rmd +++ b/rmd/30_BatchEffects.Rmd @@ -77,7 +77,7 @@ panc_sub <- UpdateSeuratObject(readRDS(fdest)) ## Seurat v5 would require this > 🧭✨ Poll: > -> [Which sequencing technologies are retained in the subset dataset?](https://PollEv.com/multiple_choice_polls/j2zBwetamS5edfxq0JDs8/respond) +> Which sequencing technologies are retained in the subset dataset? > > How many cells were sequenced in each experiment? @@ -99,7 +99,7 @@ p1 + p2 > In the previous course units, you have learned to call differentially expressed genes with Seurat. > In this task, we ask you to: - call genes differentially expressed between cells sequenced with the smartseq2 technology and those with the celseq technology - plot a violin plot for the top gene - plot a feature plot for the top gene -> 🧭✨ Poll: [What is the name of the top DE gene ?](https://PollEv.com/multiple_choice_polls/D5BfavArbiXgs8QeHvDNn/respond) +> 🧭✨ Poll: What is the name of the top DE gene ? Here's our proposed solution: @@ -214,7 +214,7 @@ gc() Let's have a brief look at the panc.combined dataset - a new Assay has been created by the integration procedure. -> 🧭✨ Poll: [What is the new assay called?]() Hint: you can access assays of a Seurat object with `Assays()`. +> 🧭✨ Poll: What is the new assay called? Hint: you can access assays of a Seurat object with `Assays()`. ## Process the newly integrated dataset diff --git a/rmd/31_SCTransform.Rmd b/rmd/31_SCTransform.Rmd index fe619e1..8907805 100644 --- a/rmd/31_SCTransform.Rmd +++ b/rmd/31_SCTransform.Rmd @@ -77,7 +77,7 @@ p2 <- FeaturePlot(ctrl, features = "nCount_RNA") + theme(legend.position = "righ p1 + p2 ``` -> 🧭✨ Poll: [Which cell population has the highest total counts?](https://PollEv.com/multiple_choice_polls/jHulGlJWYI49AaEVkAbxm/respond) +> 🧭✨ Poll: Which cell population has the highest total counts? > Hint: use the `FetchData` to retrieve variables `nCounts` and `seurat_annotations` to a data frame. Process it further with Dplyr functions: `group_by`, `summarize(total_counts = sum(nCount_RNA))`, and `arrange`. ## Seurat SCTransform @@ -131,7 +131,7 @@ ctrl_ln + ctrl_sct What has changed and what hasn't? -> 🧭✨ Poll: [What amount of standard deviation does PC1 explain after sc-transform?](https://PollEv.com/multiple_choice_polls/AQwroH3oNpZ2uQRcly2eO/respond) +> 🧭✨ Poll: What amount of standard deviation does PC1 explain after sc-transform? > Hint: Function `Stdev(object)` returns the absolute values of standard deviations for principal components. It's the analogous to `object@reductions$pca@stdev`. @@ -154,7 +154,7 @@ What has changed and what hasn't ? > ⌨🔥 Exercise: Apply SCTransform to the IfnB-stimulated dataset as well. -> 🧭✨ Poll: [What amount of standard deviation does the first PC explain after applying sc-transform to the stimulated dataset?](https://PollEv.com/multiple_choice_polls/coHM0QIGIgmNdcxkYIb0i/respond) +> 🧭✨ Poll: What amount of standard deviation does the first PC explain after applying sc-transform to the stimulated dataset? ## Prepare both datasets for integration