- Data was regressed out by passing UMI count, the percentage of mitochondrial genes, the difference between the cell cycle phases scores.
- Data was regressed out by passing UMI count, the percentage of mitochondrial genes, the difference between the cell cycle phases scores, as described in the Seurat [vignette](https://satijalab.org/seurat/articles/cell_cycle_vignette.html#alternate-workflow-1).
- Dimensionality reduction and Harmony batch removal:
- Dimensionality reduction and Harmony batch removal:
- A principal component analysis (PCA) with 100 principal components (PCs) was performed and a UMAP-representation as well as clusters were computed on the top 55 components (orig.ident as batch variable)
- A principal component analysis (PCA) with 100 principal components (PCs) was performed and a UMAP-representation as well as clusters were computed on the top 55 components (orig.ident as batch variable)