muskim
Museong Kim
Recently Published
Plot
angio topmarker
ang_celltype (3)
plot_cells_3d(cds_angio, color_cells_by = "celltype",show_trajectory_graph = F)
ang_orig.ident (2)
plot_cells_3d(cds_angio, color_cells_by = "orig.ident", show_trajectory_graph = F)
ang_angio_cluster (1)
cds_angio<-cds_3d[rowData(cds_3d)$id %in% angio_list,] cds_angio<-clear_cds_slots(cds_angio) cds_angio<-preprocess_cds(cds_angio)#, norm_method = "none") plot_pc_variance_explained(cds_angio) cds_angio <- reduce_dimension(cds_angio,max_components=3) cds_angio <- cluster_cells(cds_angio) plot_cells_3d(cds_angio, color_cells_by = "angio_clusters")
ang_UMAP
pData(cds_3d)$angio_clusters<-clusters(cds_angio)
plot_cells_3d(cds_3d, color_cells_by = "angio_clusters")
tsc1 project. (filtered samples) #6
cluster geno stage
tsc1 project. (filtered samples) #4
colored by genotype
tsc1 project. (filtered samples) #3
colored by stage.
tsc1 project. (filtered samples) #2
filter: nCount_RNA>200 & nCount_RNA<10000 &percent.mt<10
after align_cds(cds, alignment_group = "orig.ident") (orig.ident: stage_genotype)
tsc1 project. (all samples) #1
no QC. not separated by age and genotype.