Publications by Nasir Mahmood Abbasi
Pre-Analysis using FeaturePlot
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("/home/bioinfo/0-imp_Robj/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 ...
3465 sym Python (7357 sym/22 pcs) 11 img
ADT normalization- Margin = 2 and Visualized by dittoseq heatmap
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("/home/bioinfo/0-imp_Robj/All_Normal-PBMC_Abnormal-cellLines_T_cells_Merged_Annotated_UMAP_on_Clusters_to_USE.Robj") All_samples_Merged An object of class Seurat 62625 features across 46976 sample...
3098 sym R (9613 sym/12 pcs) 3 img
ADT normalization- Margin = 1 and Visualized by dittoseq heatmap
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("/home/bioinfo/0-imp_Robj/All_Normal-PBMC_Abnormal-cellLines_T_cells_Merged_Annotated_UMAP_on_Clusters_to_USE.Robj") All_samples_Merged An object of class Seurat 62625 features across 46976 sample...
4888 sym R (5437 sym/14 pcs) 3 img
Enrichment after FC Scanner Analysis-part2
1. load libraries 2. Enrichment Analysis_part1 # Load necessary libraries ------------------------------------ # Read the TSV file into R Significant_Genes <- read_csv("/home/bioinfo/18-Enrichment_Analysis_final_Results/2-filtered_All_cell_lines_cells_vs_CD4_Control.csv") Rows: 3018 Columns: 9── Column specification ────────�...
15753 sym R (11401 sym/51 pcs) 19 img
FC Scanner files for Analysis-part2
1. load libraries #Differential Expression Analysis 2. load seurat object and save metadata file for samples #Load Seurat Object L7 load("/home/bioinfo/0-imp_Robj/Harmony_integrated_All_samples_Merged_with_PBMC10x_with_harmony_clustering.Robj") # sct_data <- GetAssayData(All_samples_Merged, assay = "SCT", layer = "data") # memory.limit(size = 640...
19188 sym R (12688 sym/7 pcs)
silhouette Score Test
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") Le chargement a nécessité le package : SeuratObject Le chargement a nécessité le package : sp Attachement du package : ‘SeuratObject’ Le...
4905 sym R (4031 sym/18 pcs) 3 img
Sézary Syndrome silhouette Score Test-Part2
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 variabl...
4950 sym R (3400 sym/15 pcs) 3 img
Enrichment after FC Scanner Analysis
1. load libraries 2. Enrichment Analysis_part1 # Load necessary libraries ------------------------------------ # Read the TSV file into R Significant_Genes <- read_csv("/home/bioinfo/18-Enrichment_Analysis_final_Results/NewFiles/All_Results_Together_for_Enrichment/Cell_lines_vs_control/filtered_data_Cell_lines_vs_CD4Tcells.csv") Rows: 746 Columns...
5758 sym Python (3837 sym/16 pcs) 6 img
DE with FC Scanner
1. load libraries #Differential Expression Analysis 2. load seurat object #Load Seurat Object L7 load("/home/bioinfo/0-imp_Robj/Harmony_integrated_All_samples_Merged_with_PBMC10x_with_harmony_clustering.Robj") # sct_data <- GetAssayData(All_samples_Merged, assay = "SCT", layer = "data") # memory.limit(size = 64000) # # # Transpose the data so th...
22029 sym R (14399 sym/9 pcs)
Tables of celltypes based on cell_lines
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, 30...
4847 sym R (20279 sym/6 pcs) 4 img