EBAII n1 scRNAseq : Training intermediate Seurat (v5) objects

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