Publications by Nasir Mahmood Abbasi
WNN analysis of CITE-seq, RNA + ADT-PART5
1. load libraries 2. Load Seurat Object DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap", label.size = 3, repel = T, label = T) DimPlot(All_samples_Merged, group.by = "SCT_snn_res.0.9", reduction = "umap", label.size = 3, repel = T, label = T) cluster...
13238 sym R (26834 sym/64 pcs) 38 img
TCR Analysis-Part2
Introduction scRepertoire is designed to take filter contig outputs from the 10x Genomics Cell Ranger pipeline, process that data to assign clonotype based on two TCR or Ig chains and analyze the clonotype dynamics. The latter can be separated into 1) clonotype-only analysis functions, such as unique clonotypes or clonal space quantification, and 2...
29997 sym R (17791 sym/70 pcs) 59 img
WNN analysis of CITE-seq, RNA + ADT_part4
1. load libraries 2. Load Seurat Object DimPlot(All_samples_Merged,group.by = "cell_line", reduction = "umap", label.size = 3, repel = T, label = T) DimPlot(All_samples_Merged, group.by = "SCT_snn_res.0.9", reduction = "umap", label.size = 3, repel = T, label = T) cluster...
12514 sym R (24577 sym/59 pcs) 35 img
WNN analysis of CITE-seq, RNA + ADT part2
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 An object of class Seurat 62625 features across 46976 samples within 6 assays Active assay: SCT (25901 features, 3000 variable fea...
8694 sym R (22072 sym/49 pcs) 21 img
WNN analysis of CITE-seq, RNA + ADT
1. load libraries 2. Load Seurat Object 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, data, scale.data 5 other assays present: RNA, ADT, prediction.score.celltype.l1, prediction.score.celltype.l2, predictio...
5433 sym 5 img
WNN analysis of CITE-seq, RNA + ADT_part3
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 An object of class Seurat 62625 features across 46976 samples within 6 assays Active assay: SCT (25901 features, 3000 variable fea...
8705 sym R (21952 sym/48 pcs) 21 img
Inference and analysis of cell-cell communication using CellChat-Melange
1. load libraries 2. Load Seurat Object #Load Seurat Object Integrated Object load("Melange_v3.Robj") Melange An object of class Seurat 59684 features across 81220 samples within 3 assays Active assay: SCT (23076 features, 3000 variable features) 3 layers present: counts, data, scale.data 2 other assays present: RNA, ADT 2 dimensional reduc...
22108 sym R (113618 sym/110 pcs) 49 img
L1_Merged_first_HPC_PC-1:21-6-old_script
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("All_T_cells_Merged_filtered_Mono_using_clusters.Robj") All_samples_Merged <- filtered_data All_samples_Merged An object of class Seurat 62626 features across 46976 samples within 6 assays Active assay: SCT (25902 featu...
15502 sym R (82211 sym/81 pcs) 28 img
UMAP of T cells without other PBMC cells using clusters and PC-1:20
UMAP of T cells without other PBMC cells using clusters and PC-1:50 UMAP of T cells without other PBMC cells using clusters and PC-1:50 1. load libraries 2. Load Seurat Object 3. Azimuth Annotation 4. QC Assign Cell-Cycle Scores 5. Normalize data 6. Perform PCA 7. Perform PCA TEST 8. Clustering 9....
1136 sym Python (28508 sym/108 pcs) 31 img
SL1_Merged_first_HPC_PC-1:50-3
SS_Robj_CellLines_PBMC_Merged_without_Correction_L1_Merged_first_HPC_PC-1:50-3 SS_Robj_CellLines_PBMC_Merged_without_Correction_L1_Merged_first_HPC_PC-1:50-3 1. load libraries 2. Load Seurat Object 3. QC 4. Normalize data 5. Perform PCA Perform PCA TEST 6. Clustering 7. Azimuth Annotation 8. Cell type ...
1090 sym Python (22344 sym/121 pcs) 22 img