Update Dataset_Overview.csv

Dataset_Overview.csv

@@ -1,21 +1,21 @@
-Metric,Prostate_Cancer,Non_Cancerous
-Dataset_Type,Tumor samples,Benign samples
-Total_Cells,30932,12205
-Total_Genes,846,779
-Number_of_Samples,7,7
-Number_of_Clusters,14,14
-Seurat_Version,5.1.0,5.1.0
-Normalization_Method,LogNormalize + SCTransform,LogNormalize + SCTransform
-Integration_Method,Canonical Correlation Analysis,Canonical Correlation Analysis
-Dimensionality_Reduction,PCA + UMAP,PCA + UMAP
-Clustering_Resolution,0.5,0.5
-Variable_Features_Count,2000 (VST method),2000 (VST method)
-PCA_Dimensions_Used,01:15,01:15
-UMAP_Metric,Cosine,Cosine
-Quality_Control_Applied,Yes (multi-step),Yes (multi-step)
-Cell_Cycle_Regression,Yes (S.Score + G2M.Score),Yes (S.Score + G2M.Score)
-Doublet_Removal,Yes (scDblFinder),Yes (scDblFinder)
-Batch_Correction,Yes (SCTransform integration),Yes (SCTransform integration)
-Min_Features_Per_Cell,>500,>500
-Ribosomal_Filter_Percentile,90th percentile,90th percentile
-Mitochondrial_Filter_Percentile,90th percentile,90th percentile
+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