Publications by Nasir Mahmood Abbasi
Gene Enrichment Analysis (P1_vs_P2)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("comparison_P1_vs_P2.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, lab = Malignant_CD4Tcells_vs_Normal_CD4Tcells$gene, ...
23735 sym R (17654 sym/40 pcs) 15 img
Gene Enrichment Analysis (P1_vs_P3)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("comparison_P1_vs_P3.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, lab = Malignant_CD4Tcells_vs_Normal_CD4Tcells$gene, ...
23734 sym R (17964 sym/42 pcs) 16 img
Gene Enrichment Analysis (P2_vs_P3)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("comparison_P2_vs_P3.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, lab = Malignant_CD4Tcells_vs_Normal_CD4Tcells$gene, ...
23752 sym R (17998 sym/39 pcs) 13 img
Malignant CD4Tcells vs Control(Normal CD4 Tcells)-Enrichment_final-after_filtering
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("1-MAST_with_SCT_batch_patient_cellline_as_Covariate_with_meanExpression.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, la...
23902 sym R (18266 sym/42 pcs) 16 img
fgsea-L1 vs Control(Normal CD4 Tcells)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("All_genes_celllines_vs_normal_updated_with_mean_expression/Updated_DE_Results_L1_with_MeanExpr.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tce...
17589 sym R (11705 sym/27 pcs) 12 img
fgsea-L4 vs Control(Normal CD4 Tcells)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("2-All_genes_celllines_vs_normal_updated_with_mean_expression/Updated_DE_Results_L4_with_MeanExpr.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4T...
17608 sym R (12225 sym/29 pcs) 12 img
fgsea-L2 vs Control(Normal CD4 Tcells)
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("2-All_genes_celllines_vs_normal_updated_with_mean_expression/Updated_DE_Results_L2_with_MeanExpr.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4T...
17608 sym R (12225 sym/29 pcs) 12 img
fgsea-L3 vs Control(Normal CD4 Tcells
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("2-All_genes_celllines_vs_normal_updated_with_mean_expression/Updated_DE_Results_L3_with_MeanExpr.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4T...
17608 sym R (12225 sym/29 pcs) 12 img
Differential Expression Analysis of Malignant CD4Tcells vs Control(Normal CD4 Tcells)-GSEA-Selected_top_genes
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("../selected_DE_genes_for_DE.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, lab = Malignant_CD4Tcells_vs_Normal_CD4Tcells$...
23849 sym R (17301 sym/40 pcs) 17 img
L3 vs Control(Normal CD4 Tcells)-GSEA
1. load libraries 2. Perform DE analysis using Malignant_CD4Tcells_vs_Normal_CD4Tcells genes Malignant_CD4Tcells_vs_Normal_CD4Tcells <- read.csv("../../2-DE_on_Harmony_Integration/Filtered_DE_Results_L3_with_MeanExpr.csv", header = T) 3. Create the EnhancedVolcano plot EnhancedVolcano(Malignant_CD4Tcells_vs_Normal_CD4Tcells, lab...
23824 sym R (22039 sym/51 pcs) 17 img