Publications by Nasir Mahmood Abbasi
Harmony integrations of PBMC10x by cell_line_group-theta-0.5
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active as...
8043 sym R (8037 sym/30 pcs) 16 img
Harmony integrations of PBMC10x by sample_group-theta-0.5
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active as...
8035 sym R (7946 sym/30 pcs) 16 img
Sézary Syndrome Cell Line Analysis-DE-Integrated
1. load libraries #Differential Expression Analysis 2. load seurat object #Load Seurat Object L7 load("../../0-IMP-OBJECTS/Harmony_integrated_All_samples_Merged_with_PBMC10x.Robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active assay: SCT (27417 features, 3000 variable features) 3 layers...
30747 sym R (30944 sym/170 pcs) 30 img
Sézary Syndrome Cell Line Analysis-DE-PBMC10X
1. load libraries #Differential Expression Analysis 2. load seurat object #Load Seurat Object L7 load("../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active assay: SCT (27417 features, 3000 variable features) 3 la...
30609 sym R (30829 sym/169 pcs) 29 img
Harmony integrations of PBMC10x-part4
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active as...
16979 sym R (18880 sym/69 pcs) 37 img
Differential Expression Analysis of SS vs PBMC10X+PBMC
1. load libraries 2. Load Seurat Object All_samples_Merged <- SetIdent(All_samples_Merged, value = "cell_line") DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap", label.size = 3, repel = T, label = T) DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap.harmony", ...
25727 sym R (26688 sym/69 pcs) 29 img
Multiple Harmony integrations of PBMC10x-part3
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged 3. Data PREPARATION and Harmony Integration-1 library(harmony) All_samples_Merged <- R...
23762 sym R (15748 sym/13 pcs)
Multiple Harmony integrations of PBMC10x
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active as...
22580 sym R (27809 sym/92 pcs) 39 img
Harmony integrations of PBMC10x bu sample group, cell line group and cell line
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active as...
6014 sym R (4052 sym/10 pcs) 7 img
Harmony Integration of PBMC10x-part2
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration SS_All_samples_Merged <- load("../../../0-IMP-OBJECTS/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples w...
5210 sym Python (7650 sym/22 pcs) 7 img