Comments (2)
Hi ti-spat,
Thanks for trying out our demonstration tutorials and your feedback. There are currently a number of different ways you can perform cell type enrichment within Giotto:
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based on single-cell RNA-seq normalized count matrix and an accompanying vector of cell cluster annotations for that dataset:
You could then use makeSignMatrixRank to create a rank matrix and use this as input for runRankEnrich -
based on lists of cell type specific marker genes:
You could then provide these lists of cell type specific marker genes to makeSignMatrixPage to create a matrix that can be used as input for runPAGEEnrich -
Similar as to point 2 you can also run a simple runHyperGeometricEnrich test
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Finally, you can perform deconvolution using single-cell RNA-seq data with the function runDWLSDeconv function. This is still in the beta-phase, but we're seeing pretty good results.
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Alternatively, you can also use some of the other methods that have been recently published to perform deconvolution and then transfer the results to Giotto. This probably requires a little bit more work, but I'm happy to assist.
I'll try to create a HOWTO for these different options in the near future. It's on my to-do list and will be available here: https://rubd.github.io/Giotto_site/articles/tut7_giotto_enrichment.html
Best
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Hi Ruben,
Thanks for quick, kind and detail instructions!
I'd like to try these methods using suggested functions in order.
I also look forward updates!
Best
from giotto.
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