BestPracticesST
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Add workflow chapter on a cancer dataset
Add a workflow chapter on a cancer dataset, e.g. one of the publicly available human breast cancer datasets from 10x Genomics.
Cancer datasets require some adaptations to our existing analysis pipelines due to the different data characteristics. For example:
- cancer datasets contain highly distinct cell types, i.e. immune, stroma, cancer
- immune cells are very small (around 5 um), so we may have up to 5-10 cells per Visium spot
- cell types are highly interspersed, so individual spots contain highly distinct cell types - so spot-level deconvolution will be important (either using existing spot-level deconvolution methods or more general deconvolution methods for cancer based on CNVs / SNPs etc)