Preprocessing that happens to added datasets.
The OSCA handbook was used to guide preprocessing choices.
kallisto v0.46.0 is used for pseudo-quantification with an index built using GRCh38 release 94.
kallisto bustools is up to 51 times faster than Cell Ranger and runs in constant memory.
Highly variable genes are within the top 10% of biological variance.
Dimensionality reduction and clustering
The top 30 principle components are used to detect clusters and generate UMAP plots.
Clustering uses the leiden algorithm and the resolution parameter can be adjusted.