EBAII n1 scRNAseq : Training intermediate Seurat (v5) objects

Intermediate Seurat (v5) objects produced for the EBAII n1 single cell RNAseq training. 01_TD3A_S5_Metrics.Tech_31053.4587.RDS : Technical metrics (nFeature, nCount, ...) 02_TD3A_S5_Metrics.All_31053.4587.RDS : Biological metrics (%mito, %ribo, %stress) 03_TD3A_S5_CC_31053.4587.RDS : Estimated cell cycles scores and phase 04_TD3A_S5_Metrics.Filtered_12508.4278.RDS : Cells and features filtered according to metrics 05_TD3A_S5_Doublets.filtered_12508.4035.RDS : Cell doublets removed 06_TD3A_S5_LogNorm_12508.4035.RDS : LogNormalization applied 07_TD3A_S5_Scaled.2k_12508.4035.RDS : Scaling using 2000 HVGs 08_TD3A_S5_Scaled.2k_Reg.PCrb_12508.4035.RDS : Same with regression for percent_rb (% ribo) 09_TD3A_S5_DimRed.PCA_12508.4035.RDS : PCA with 50 components 10_TD3A_S5_Clustered.0.8_12508.4035.RDS : Louvain clustering with resolution 0.8 11_TD3A.TDCT_S5_Merged_12926.3886 : Merging of the pre-processed TD3A and TDCT samples (each halved for its cells, using random subsampling with the seed 1337) 12_TD3A.TDCT_S5_Integrated_12926.3886.RDS : Results of TD3A and TDCT samples integration using 4 different methods (Seurat's CCA, RPCA, Harmony ; and standalone Harmony), and Louvain clustering for each (res 0.8) 13_TD3A.TDCT_S5_Integrated_Annotated.RDS : Results of the automatic cell type annotation