Publications by Nasir Mahmood Abbasi
Tables of celllines based on clusters harmony0.9
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 ...
3728 sym R (3854 sym/12 pcs) 4 img
Tables of celltypes based on clusters harmony0.9
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 ...
8788 sym R (25592 sym/28 pcs) 8 img
Cell_lines vs PBMC
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 ...
48641 sym R (42473 sym/147 pcs) 44 img
Patients vs PBMC-Tcells
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...
23757 sym R (19979 sym/72 pcs) 26 img
TCR Analysis using harmony integrated UMAP
1. 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, an...
39421 sym R (129932 sym/94 pcs) 80 img
Cell Line derived from each patient DE comparison-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 v...
21611 sym R (18396 sym/69 pcs) 14 img
Significant genes for strings
1. load libraries 2. Significat genes and up and down 3. VolcanoPlot LS0tCnRpdGxlOiAiU2lnbmlmaWNhbnQgZ2VuZXMgZm9yIHN0cmluZ3MiCmF1dGhvcjogTmFzaXIgTWFobW9vZCBBYmJhc2kKZGF0ZTogImByIFN5cy5EYXRlKClgIgpvdXRwdXQ6CiAgI3JtZGZvcm1hdHM6OnJlYWR0aGVkb3duCiAgaHRtbF9ub3RlYm9vazoKICAgIHRvYzogdHJ1ZQogICAgdG9jX2Zsb2F0OiB0cnVlCiAgICB0b2NfY29sbGFwc2VkOiB0cnVlCi0tLQ...
3194 sym
Sézary Syndrome Cell Line derived from each patient DE comparison
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...
26900 sym R (15559 sym/58 pcs) 27 img
Sézary Syndrome Cell Line Top5 gene markers
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...
13865 sym 2 img