diff --git a/episodes/cell_type_annotation.Rmd b/episodes/cell_type_annotation.Rmd index c2a8feb..78b2c02 100644 --- a/episodes/cell_type_annotation.Rmd +++ b/episodes/cell_type_annotation.Rmd @@ -83,17 +83,15 @@ which the cells truly reside. After annotation based on marker genes, the clusters can be treated as proxies for more abstract biological concepts such as cell types or states. -Popularized by its use in -[Seurat](https://cran.r-project.org/web/packages/Seurat/index.html), -graph-based clustering is a flexible and scalable technique for -clustering large scRNA-seq datasets. We first build a graph where each -node is a cell that is connected to its nearest neighbors in the -high-dimensional space. Edges are weighted based on the similarity -between the cells involved, with higher weight given to cells that are -more closely related. We then apply algorithms to identify "communities" -of cells that are more connected to cells in the same community than -they are to cells of different communities. Each community represents a -cluster that we can use for downstream interpretation. +Graph-based clustering is a flexible and scalable technique for identifying +coherent groups of cells in large scRNA-seq datasets. We first build a graph +where each node is a cell that is connected to its nearest neighbors in the +high-dimensional space. Edges are weighted based on the similarity between the +cells involved, with higher weight given to cells that are more closely related. +We then apply algorithms to identify "communities" of cells that are more +connected to cells in the same community than they are to cells of different +communities. Each community represents a cluster that we can use for downstream +interpretation. Here, we use the `clusterCells()` function from the [scran](https://bioconductor.org/packages/scran) package to perform @@ -549,12 +547,6 @@ AUCell_exploreThresholds(cell.aucs[10:18], plotHist = TRUE, assign = TRUE) :::: -## Session Info - -```{r sessionInfo} -sessionInfo() -``` - ## Exercises ::: challenge @@ -720,3 +712,9 @@ Remember, this is an exploratory diagnostic, not the final word! At this point i - The `r Biocpkg("AUCell")` package provides an enrichment test to identify curated marker sets that are highly expressed in each cell. ::: + +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` diff --git a/episodes/eda_qc.Rmd b/episodes/eda_qc.Rmd index c251066..3e64712 100644 --- a/episodes/eda_qc.Rmd +++ b/episodes/eda_qc.Rmd @@ -808,3 +808,10 @@ Mathematically, this would require the data to fall on a two-dimensional plane ( [^2]: [Vallejos (2017)](learners/reference.md#litref) [^3]: [Lun (2016)](learners/reference.md#litref) +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` + + diff --git a/episodes/hca.Rmd b/episodes/hca.Rmd index a7fbac6..a836d15 100644 --- a/episodes/hca.Rmd +++ b/episodes/hca.Rmd @@ -347,3 +347,8 @@ You can see we don't get very many cells given the strict set of conditions we u :::::::::::::::::::::::::::::::::::::::::::::::: +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` diff --git a/episodes/intro-sce.Rmd b/episodes/intro-sce.Rmd index 5370dc4..2b7b6c1 100644 --- a/episodes/intro-sce.Rmd +++ b/episodes/intro-sce.Rmd @@ -314,3 +314,9 @@ combined_sce 1. Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A single-cell molecular map of mouse gastrulation and early organogenesis. Nature 566, 7745:490-495. +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` + diff --git a/episodes/large_data.Rmd b/episodes/large_data.Rmd index 4db4a26..63d5a07 100644 --- a/episodes/large_data.Rmd +++ b/episodes/large_data.Rmd @@ -540,12 +540,6 @@ The resulting H5AD file can then be read into Python using scanpy's [read_h5ad](https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_h5ad.html) function and then directly used in compatible Python-based analysis frameworks. -## Session Info - -```{r sessionInfo} -sessionInfo() -``` - ## Exercises @@ -646,3 +640,9 @@ system.time({i.out <- runPCA(sce.brain, - Converter functions between existing single-cell data formats enable analysis workflows that leverage complementary functionality from poplular single-cell analysis ecosystems. :::::::::::::::::::::::::::::::::::::::::::::::: + +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` diff --git a/episodes/multi-sample.Rmd b/episodes/multi-sample.Rmd index dec4520..d049f17 100644 --- a/episodes/multi-sample.Rmd +++ b/episodes/multi-sample.Rmd @@ -483,12 +483,6 @@ topTags(res.lfc) Addionally, the choice of \tau can be guided by other external experimental data, like a previous or a pilot experiment. -## Session Info - -```{r, tidy=TRUE} -sessionInfo() -``` - ## Exercises @@ -585,7 +579,7 @@ If there were large shifts in the logFC estimates or p-value distributions, that #### Extension challenge 1: Group effects -Having multiple independent samples in each experimental group is always helpful, but it particularly important when it comes to batch effect correction. Why? +Having multiple independent samples in each experimental group is always helpful, but it's particularly important when it comes to batch effect correction. Why? ::: solution @@ -625,3 +619,10 @@ Imagine you had one sample that received a drug treatment and one that did not, limited replication - except that the counts are not of reads per gene, but of cells per label. :::::::::::::::::::::::::::::::::::::::::::::::: + +## Session Info + +```{r, tidy=TRUE} +sessionInfo() +``` +