@@ -58,12 +58,12 @@ scRNAseq analysis was performed with [Seurat](https://satijalab.org/seurat/). Be
...
@@ -58,12 +58,12 @@ scRNAseq analysis was performed with [Seurat](https://satijalab.org/seurat/). Be
2. Cell cycle scoring
2. Cell cycle scoring
3. Normalization (default seurat settings)
3. Normalization (default seurat settings)
4. Scaling (with following variables to regress out: percent.mt + nCount_RNA and CC.Difference calculated as show in [vignette](https://satijalab.org/seurat/articles/cell_cycle_vignette.html#alternate-workflow-1))
4. Scaling (with following variables to regress out: percent.mt + nCount_RNA and CC.Difference calculated as show in [vignette](https://satijalab.org/seurat/articles/cell_cycle_vignette.html#alternate-workflow-1))
4. Dimensionality reduction: PCA
5. Dimensionality reduction: PCA
5. Clustering
6. Clustering
6. Markers identification
7. Markers identification
- [6.1] Clusters related markers
- [7.1] Clusters related markers
- [6.2] Intracluster differential expression analysis according to comparison of interest
- [7.2] Intracluster differential expression analysis according to comparison of interest
Pseudotime analysis was performed using [Monocle3](http://cole-trapnell-lab.github.io/monocle3/) and PAGA-tree from [dynverse](https://dynverse.org/)
Pseudotime analysis was performed using [Monocle3](http://cole-trapnell-lab.github.io/monocle3/) and PAGA-tree from [dynverse](https://dynverse.org/)
