Table 3 Analysis of the seven scRNA-seq datasets in R Seurat- workflow.
From: An integrated single-cell transcriptomic dataset for non-small cell lung cancer
Dataset | GSE131907 | GSE136246 | GSE148071 | GSE153935 | KU_loom | GSE127465 | GSE119911 |
|---|---|---|---|---|---|---|---|
Step 1: QC | nFeature_RNA > 200 & < 3000; Percent_mt <20 | ||||||
| Â | Step 2: Normalization | ||||||
| Â | Step 3: Identification of variable features | ||||||
| Â | Step 4: Scaling the data | ||||||
| Â | Step 5: PCA dimensional reduction | ||||||
Step 6: Determine no. of PCs | 20 | 20 | 20 | 20 | 20 | 20 | 20 |
| Â | Step 7: Cell clustering | ||||||
| Â | Step 8: UMAP plotting | ||||||
Step 9: Cell type annotation | Annotation provided | Annotation provided | Own annotation | Own annotation | Own annotation | Annotation provided | Own annotation |
