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Add bluster functions to cheatsheet #814

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add kmeans and nngraph functions
sjspielman committed Dec 2, 2024

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commit c51a4437e6eaf8eb575c3a8307c667a4c4365464
2 changes: 2 additions & 0 deletions module-cheatsheets/scRNA-seq-advanced-cheatsheet.md
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@@ -238,6 +238,8 @@ Read the [`bluster` package documentation](https://rdrr.io/bioc/bluster/) and vi
| 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`| [`KGraphParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering | Run k-means clustering using `kmeans()` when provided to `bluster::clusterRows()` |
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| `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering | Run community detection algorithms on a nearest-neighbor (NN) graph when provided to `bluster::clusterRows()` |
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| `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 |
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15 changes: 15 additions & 0 deletions module-cheatsheets/scRNA-seq-cheatsheet.md
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- [`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)

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<div style="page-break-after: always;"></div>


### `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`| [`KGraphParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering | Run k-means clustering using `kmeans()` when provided to `bluster::clusterRows()` |
| `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering | Run community detection algorithms on a nearest-neighbor (NN) graph when provided to `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/).
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