Publications by Nasir Mahmood Abbasi
Sézary Syndrome SCpubr Visualization
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_with_harmony_clustering.Robj") All_samples_Merged An object of class Seurat 64169 features across 59355 samples within 6 assays Active assay: SCT (27417 features, 3000 v...
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Sézary Syndrome top10 Clusters
1. load libraries #Differential Expression Analysis 2. load seurat object 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 present: counts, data, scale.data 5 other assays present: RNA, ADT, prediction.score.celltype.l1, predict...
33392 sym R (118094 sym/21 pcs) 3 img
Differential Expression Analysis of SS vs PBMC10X+PBMC
1. load libraries 2. Significat genes and up and down # Filter significant genes significant_genes <- data %>% filter(p_val_adj < 0.05) # Identify upregulated genes upregulated_genes <- significant_genes %>% filter(avg_log2FC > 1.5) # Identify downregulated genes downregulated_genes <- significant_genes %>% filter(avg_log2FC < -1.5) 3. Volcano...
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DE_Harmony_integrated_0.9_SS vs PBMC10X+PBMC_Tcells
1. load libraries 2. Load Seurat Object load ("/home/bioinfo/0-imp_Robj/Harmony_integrated_All_samples_Merged_with_PBMC10x_with_harmony_clustering.Robj") 2. Initial Visualization All_samples_Merged <- SetIdent(All_samples_Merged, value = "Harmony_snn_res.0.9") DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap.harmon...
22704 sym R (20337 sym/54 pcs) 21 img
Differential Expression Analysis
1. load libraries 2. Load Seurat Object load("/home/bioinfo/0-imp_Robj/Harmony_integrated_All_samples_Merged_with_PBMC10x_with_harmony_clustering.Robj") 3. Initial Visualization All_samples_Merged <- SetIdent(All_samples_Merged, value = "Harmony_snn_res.0.9") DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap.harmony...
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InferCNV Analysis
1. load libraries 2. perform infercnv operations to reveal cnv signal ##this is to match the chr-regions to the chr-arms hg38 = read.delim("../cytoBand_hg38.txt", header = F) cnv = read.table("../L1/HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat",header = T) ##from inferCNV resulting files cytoband = hg3...
27663 sym R (22100 sym/40 pcs) 5 img
Harmony_Intergrations_and_visualization_of_PBMC-10x.
1. load libraries 2. Load Seurat Object and visualize harmonyintegrated_UMAP #Load Seurat Object merged from cell lines and a control(PBMC) after filtration 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 Acti...
10854 sym R (37990 sym/73 pcs) 31 img
Harmony integrations of PBMC10x by cell_line-theta-Default
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...
8011 sym R (8260 sym/30 pcs) 16 img
Harmony integrations of PBMC10x by cell_line-theta-0
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...
8019 sym R (7942 sym/30 pcs) 16 img
Harmony integrations of PBMC10x by cell_line-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...
8027 sym R (7944 sym/30 pcs) 16 img