Commit 70149e0c authored by Giorgia Giacomini's avatar Giorgia Giacomini
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Update README.md

parent 584d943d
...@@ -11,7 +11,7 @@ scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/ ...@@ -11,7 +11,7 @@ scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/
- Normalization - Normalization
- Default Seurat settings [(NormalizeData function)](https://satijalab.org/seurat/reference/normalizedata) - Default Seurat settings [(NormalizeData function)](https://satijalab.org/seurat/reference/normalizedata)
- Scaling: - Scaling:
- 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)
- Clustering - Clustering
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