cswoboda

Also struggling with the same thing!

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When you create your Seurat object, you specify min.features = 200. That means any cells in your count matrices that have less than 200 features will be subset. If you...

Hi, not the developers, but harmony does not calculate a corrected expression matrix for genes. You can try using the package SC Merge like recommended in that review!

@JJBio Harmony corrects the PCA in order to perform integration. The underlying gene expression values should be "non-corrected" as harmony only uses them to produce clusters and the integrated UMAP,...

@JJBio Sorry I may be a bit confused, are you referring to the review posted? In terms of what I'm aware of as standard practice within the field, the Seurat...

Hello, not the dev team, but are you both specifying the dims in this format "1:20" for example, and not just using dims.use = 20? I had the same issue...

Hi both, not the package maintainer but this shouldnt be an issue for this type of integration. You start with the raw count matrices before integration. Truly, I find it...

Hey Delia, Cells.in.well is an object placed into the meta data that's used by the tutorial. If you're using your own data, if you don't have that meta data (as...