diff --git a/module-cheatsheets/scRNA-seq-advanced-cheatsheet.md b/module-cheatsheets/scRNA-seq-advanced-cheatsheet.md index 64346cda..f21ede26 100644 --- a/module-cheatsheets/scRNA-seq-advanced-cheatsheet.md +++ b/module-cheatsheets/scRNA-seq-advanced-cheatsheet.md @@ -22,6 +22,7 @@ If you have a different version of R or other R packages, the documentation may - [`scater`](#scater) - [`miQC`](#miqc) +- [`batchelor` and `harmony`](#batchelor-and-harmony) - [`SingleR`](#singler) - [`pheatmap` and `EnhancedVolcano`](#pheatmap-and-enhancedvolcano) - [`DESeq2` and pseudo-bulking functions](#deseq2-and-pseudo-bulking-functions) @@ -33,6 +34,7 @@ If you have a different version of R or other R packages, the documentation may - [`msigdbr`](#msigdbr) - [`clusterProfiler` and `enrichplot`](#clusterprofiler-and-enrichplot) - [`AUCell` and `GSEABase`](#aucell-and-gseabase) +- [`bluster`](#bluster) @@ -219,8 +221,25 @@ Read the [`AUCell` package documentation](https://bioconductor.org/packages/rele |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| | `GSEABase` | [`GeneSet()`](https://rdrr.io/bioc/GSEABase/man/GeneSet-class.html) | Gene set | Constructs a gene set as a `GeneSet` object for use with `AUCell` | | `GSEABase` | [`GeneSetCollection()`](https://rdrr.io/bioc/GSEABase/man/GeneSetCollection-class.html) | Gene set collection | Constructs a collection of gene sets as a `GeneSetCollection` object for use with `AUCell` -| `AUCell` | [`AUCell_buildRankings()`](https://rdrr.io/bioc/AUCell/man/AUCell_buildRankings.html) | Build cell rankings | Builds a ranking of genes for each cell that is used to calculate the recovery curve | +| `AUCell` | [`AUCell_buildRankings()`](https://rdrr.io/bioc/AUCell/man/AUCell_buildRankings.html) | Build cell rankings | Builds a ranking of genes for each cell that is used to calculate the recovery curve | | `AUCell` | [`AUCell_calcAUC()`](https://rdrr.io/bioc/AUCell/man/AUCell_calcAUC.html) | Calculate AUC | Calculates the area under the recovery curve (AUC) for each gene set in each cell | | `AUCell` | [`AUCell_exploreThresholds()`](https://rdrr.io/bioc/AUCell/man/AUCell_exploreThresholds.html) | Explore thresholds | Calculates thresholds in AUC values that can be used to assign cells; optionally makes assignments and produces histograms | + +## `bluster` + +Read the [`bluster` package documentation](https://rdrr.io/bioc/bluster/) and vignettes on its usage: + +* [Flexible clustering for Bioconductor](https://rdrr.io/bioc/bluster/f/vignettes/clusterRows.Rmd) +* [Assorted clustering diagnostics](https://rdrr.io/bioc/bluster/f/vignettes/diagnostics.Rmd) + + +| Library/Package | Piece of Code | What it's called | What it does | +|----------------------|--------------------|---------------------|---------------| +| `bluster`| [`clusterRows()`](https://rdrr.io/bioc/bluster/man/clusterRows.html)| Cluster rows of a matrix | Perform clustering using a variety of algorithms on a matrix-like object | +| `bluster`| [`KmeansParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering parameters | Set up parameters to run clustering using `kmeans()` within `bluster::clusterRows()` | +| `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering parameters | Set up parameters for nearest-neighbor (NN) graph-based clustering algorithms within `bluster::clusterRows()` | +| `bluster`| [`approxSilhouette()`](https://rdrr.io/bioc/bluster/man/approxSilhouette.html)| Approximate silhouette width | Calculate an approximate silhouette width for each cell given a set of clusters | +| `bluster`| [`neighborPurity()`](https://rdrr.io/bioc/bluster/man/neighborPurity.html)| Compute neighborhood purity | Calculate neighborhood purity for each cell given a set of clusters | +| `bluster`| [`bootstrapStability()`](https://rdrr.io/bioc/bluster/man/bootstrapStability.html)| Assess cluster stability by bootstrapping | Generate cluster bootstrap replicates to estimate cluster robustness to sampling noise | diff --git a/module-cheatsheets/scRNA-seq-advanced-cheatsheet.pdf b/module-cheatsheets/scRNA-seq-advanced-cheatsheet.pdf index c4067a7f..ed82b97b 100644 Binary files a/module-cheatsheets/scRNA-seq-advanced-cheatsheet.pdf and b/module-cheatsheets/scRNA-seq-advanced-cheatsheet.pdf differ diff --git a/module-cheatsheets/scRNA-seq-cheatsheet.md b/module-cheatsheets/scRNA-seq-cheatsheet.md index dd396ed0..77e1ca53 100644 --- a/module-cheatsheets/scRNA-seq-cheatsheet.md +++ b/module-cheatsheets/scRNA-seq-cheatsheet.md @@ -18,6 +18,7 @@ If you have a different version of R or other R packages, the documentation may - [`SingleCellExperiment`, `txmimeta`, and `DropletUtils`](#singlecellexperiment-txmimeta-and-dropletutils) - [`scran` and `scater`](#scran-and-scater) - [`purrr`, `stringr`, and `tibble`](#purrr-stringr-and-tibble) +- [`bluster`](#bluster) - [`SingleR`](#singler) @@ -154,6 +155,20 @@ purrr::map(
+ +### `bluster` + +Read the [`bluster` package documentation](https://rdrr.io/bioc/bluster/) and [this vignette](https://rdrr.io/bioc/bluster/f/vignettes/clusterRows.Rmd) on its usage. + + +| Library/Package | Piece of Code | What it's called | What it does | +|----------------------|--------------------|---------------------|---------------| +| `bluster`| [`clusterRows()`](https://rdrr.io/bioc/bluster/man/clusterRows.html)| Cluster rows of a matrix | Perform clustering using a variety of algorithms on a matrix-like object | +| `bluster`| [`KmeansParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering parameters | Set up parameters to run clustering using `kmeans()` within `bluster::clusterRows()` | +| `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering parameters | Set up parameters for nearest-neighbor (NN) graph-based clustering algorithms within `bluster::clusterRows()` | + + + ### `SingleR` Read the [`SingleR` package documentation](https://rdrr.io/bioc/SingleR/), and an [e-book on its usage](http://bioconductor.org/books/release/SingleRBook/). diff --git a/module-cheatsheets/scRNA-seq-cheatsheet.pdf b/module-cheatsheets/scRNA-seq-cheatsheet.pdf index ea8b75c5..45b88b9a 100644 Binary files a/module-cheatsheets/scRNA-seq-cheatsheet.pdf and b/module-cheatsheets/scRNA-seq-cheatsheet.pdf differ