Publications by Nasir Mahmood Abbasi
Merged All samples with PBMC_10x and SCT analysis on annotated Object
1. load libraries Le chargement a nécessité le package : SeuratObject Le chargement a nécessité le package : sp Attachement du package : ‘SeuratObject’ Les objets suivants sont masqués depuis ‘package:base’: intersect, t Registered S3 methods overwritten by 'htmltools': method from print.html ...
18684 sym R (144793 sym/58 pcs) 9 img
Merging all our cell lines and controls(PBMC-PBMC10x) into single seurat object-Robj
1.load libraries 2.Read Seurat object and Merge load("/home/bioinfo/Documents/1-SS-STeps/4-Analysis_and_Robj_Marie/analyse juillet 2023/ObjetsR/L1.Robj") load("/home/bioinfo/Documents/1-SS-STeps/4-Analysis_and_Robj_Marie/analyse juillet 2023/ObjetsR/L2.Robj") load("/home/bioinfo/Documents/1-SS-STeps/4-Analysis_and_Robj_Marie/analyse juillet 2023/...
4254 sym
PBMC_10x
1. load libraries 2. Reading Data from 10x & Creating Seurat Object # Reading 10x data and creating Seurat object sc.data <- Read10X(data.dir = "filtered_feature_bc_matrix/") # Renaming barcodes to prevent conflicts if merging later colnames(sc.data) <- paste('PBMC_10x', colnames(sc.data), sep = '_') # Creating the Seurat object from the RNA cou...
4602 sym Python (2359 sym/16 pcs) 9 img
Cytogenetic Analysis
1. load libraries 2. Data PREPERATION # Read the inferCNV HMM .dat file infercnv_data <- read.delim("../L7_PBMC_uphyloplot/HMM_CNV_predictions.HMMi6.leiden.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat", sep="\t", header=TRUE) # Remove any rows with NA or infinite values infercnv_data <- infercnv_data[complete.cases(infercnv_data), ] infercn...
17520 sym R (12115 sym/13 pcs) 2 img
Sézary Syndrome Cell Line DE Analysis
1. load libraries #Differential Expression Analysis 2. load seurat object #Load Seurat Object L7 load("../../0-IMP-OBJECTS/All_CD4_Tcells_Merged_1-13_res-0.9.Robj") All_samples_Merged An object of class Seurat 62625 features across 46976 samples within 6 assays Active assay: SCT (25901 features, 3000 variable features) 3 layers present: counts...
24649 sym R (21649 sym/123 pcs) 29 img
Phylogeny_based on inferCNV
1. load libraries 2. Load Seurat Object # load("/home/bioinfo/Cluster_to_Computer_Transfer_files_folder/All_Normal-PBMC_Abnormal-cellLines_T_cells_Merged_Annotated_UMAP_on_Clusters_to_USE.Robj") library(ape) library(dendextend) library(ggplot2) library(dplyr) # Read the observation groupings groupings <- read.table("L1_L2_P1_inferCNV/infercnv.ob...
9368 sym R (6128 sym/13 pcs) 4 img
Phylogeny_based on RNA Expression-euclidean_pearson
1. load libraries 2. Load Seurat Object load("/home/bioinfo/Cluster_to_Computer_Transfer_files_folder/All_Normal-PBMC_Abnormal-cellLines_T_cells_Merged_Annotated_UMAP_on_Clusters_to_USE.Robj") 3. Phylogeney of RNA based Expression-eucleadian DefaultAssay(All_samples_Merged) <- 'SCT' # 1. Calculate average expression for each gene in each cell l...
7986 sym R (5850 sym/40 pcs) 4 img
Differential Expression Analysis at 0.9
1. load libraries 2. Load Seurat Object load("/home/bioinfo/Cluster_to_Computer_Transfer_files_folder/All_Normal-PBMC_Abnormal-cellLines_T_cells_Merged_Annotated_UMAP_on_Clusters_to_USE.Robj") All_samples_Merged <- SetIdent(All_samples_Merged, value = "cell_line") DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap", ...
26278 sym R (18061 sym/50 pcs) 27 img
WNN analysis of CITE-seq, RNA + ADT-Part2
1. load libraries 2. Load Seurat Object load("../5-SS_ScRNA_Data_Analysis/4-ScSS_MyAnalysis_on_SS/0-Important_R_OBJ/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 samples within 6 assays Active assay: SCT (25901 features, 300...
20405 sym R (20058 sym/74 pcs) 40 img
Inference and analysis of cell-cell communication using CellChat-SS_cellLines
1. load libraries 2. Load Seurat Object #Load Seurat Object Integrated Object load("/home/bioinfo/Cluster_to_Computer_Transfer_files_folder/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 samples within 6 assays Active assay: S...
22636 sym R (105750 sym/102 pcs) 49 img