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gongx030 / ensemblemerge

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Add a `BaseNormalize` class and add support for sctransform #27

Closed gongx030 closed 2 years ago

gongx030 commented 2 years ago

Paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1874-1 R package: https://satijalab.org/seurat/articles/sctransform_vignette.html

gongx030 commented 2 years ago

Need to examine how to integrate data by using the SCTransform pipeline. SCTransform returns the batch wise scaled data, and what is the best way to combine into a full matrix of scaled data?

gongx030 commented 2 years ago

Need to examine how to integrate data by using the SCTransform pipeline. SCTransform returns the batch wise scaled data, and what is the best way to combine into a full matrix of scaled data?

See

https://swaruplab.bio.uci.edu/tutorial/integration/integration_tutorial.html#sctransform

Use vars.to.regress to regress out the batch effects.