Metric,Prostate_Cancer,Non_Cancerous,Allen_MTG,GBM_Malignant
Dataset_Type,Tumor samples,Benign samples,Adult cortex (neurotypical),Adult malignant GBM (SS2)
Total_Cells,30932,12205,13616,4916
Total_Genes,846,779,50281 (1328 integrated),23686
Number_of_Samples,7,7,8,20
Number_of_Clusters,14,14,17,4 (AC; MES; NPC; OPC)
Seurat_Version,5.1.0,5.1.0,5.3.0,5.3.0
Normalization_Method,LogNormalize + SCTransform,LogNormalize + SCTransform,LogNormalize + SCTransform,LogNormalize (pre-clustering)
Integration_Method,Canonical Correlation Analysis,Canonical Correlation Analysis,Canonical Correlation Analysis,N/A (published annotations used)
Dimensionality_Reduction,PCA + UMAP,PCA + UMAP,PCA + UMAP,N/A
Clustering_Resolution,0.5,0.5,0.5,N/A
Variable_Features_Count,2000 (VST method),2000 (VST method),1328 (integration features),2000 (VST method)
PCA_Dimensions_Used,1:15,1:15,1:8,N/A
UMAP_Metric,Cosine,Cosine,Cosine,N/A
Quality_Control_Applied,Yes (multi-step),Yes (multi-step),Yes (multi-step),Yes (Neftel et al. pipeline)
Cell_Cycle_Regression,Yes (S.Score + G2M.Score),Yes (S.Score + G2M.Score),Yes (S.Score + G2M.Score),Scored only (G1S + G2M)
Doublet_Removal,Yes (scDblFinder),Yes (scDblFinder),Yes (scDblFinder),N/A (published data)
Batch_Correction,Yes (SCTransform integration),Yes (SCTransform integration),Yes (SCTransform integration),N/A
Min_Features_Per_Cell,>500,>500,>500,N/A (Neftel QC)
Ribosomal_Filter_Percentile,90th percentile,90th percentile,90th percentile,N/A
Mitochondrial_Filter_Percentile,90th percentile,90th percentile,90th percentile,N/A