Add neighborhood analysis module functions to cheatsheet - #1066
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This all looks good to me, just a few comments:
- let's also add the function
scater::isOutlier() - I think it would be good to reorganize this so the spatial package are towards the top. For this I'd recommend moving SpatialExperimentIO and hoodscanR beneath spacexr (so you'll want to re-doctoc too)
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LGTM! One additional change needed to make the cheatsheet (and rendered pdf) say scuttle too if that's how we're using it in the notebook, but I don't need to see it again.
| | `scran`| [`getTopHVGs()`](https://rdrr.io/bioc/scran/man/getTopHVGs.html)| Get top highly variable genes | Identify variable genes in a `SingleCellExperiment` object, based on variance | | ||
| | `scran`| [`modelGeneVar()`](https://rdrr.io/bioc/scran/man/modelGeneVar.html)| model per gene variance | Model the per gene variance of a `SingleCellExperiment` object | | ||
| | `scran`| [`clusterCells()`](https://rdrr.io/github/MarioniLab/scran/man/clusterCells.html)| Cluster cells | Perform clustering on an SCE object using the `bluster` package | | ||
| | `scater`| [`isOutlier()`](https://rdrr.io/bioc/scuttle/man/isOutlier.html)| Identify outliers | Convenience function to determine which values in a numeric vector are outliers based on the median absolute deviation (MAD) | |
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I assume you mean for this to be scuttle? Also, would want to move this higher up in the table to be with the other scuttles.
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Closes #1021
This PR updates the spatial cheatsheet to include packages/functions used in the neighborhood analysis module. This includes
SpatialExperimentIO,ComplexHeatmap, andhoodscanR. Let me know if I missed anything!While here I caught a small typo where we still mentioned using
SpaceTrooperin the Xenium notebook, which we ended up taking out so I fixed that.