Publications by Nasir Mahmood Abbasi
ADT Normalization
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("../6-ADT_Normalization/All_Samples_Merged_NormalizedADT-scaled.Robj") All_samples_Merged An object of class Seurat 63193 features across 49193 samples within 6 assays Active assay: ADT (28 featu...
7127 sym Python (5297 sym/47 pcs) 32 img
UMAP-0.7 with Annotation
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration and Annotation SS_All_samples_Merged <- load("SS_All_Sample_Merged_Azimuth_ProjectTils_singleR_ANNOTATION_on_My_UMAP0.7_HPC.Robj") All_samples_Merged An object of class Seurat 63193 features across 49193 samples within 6 assay...
13135 sym Python (8433 sym/34 pcs) 27 img
ADT_Normalization
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("All_Samples_Merged_NormalizedADT.Robj") All_samples_Merged An object of class Seurat 63193 features across 49193 samples within 6 assays Active assay: RNA (36601 features, 0 variable features) ...
3545 sym Python (2591 sym/19 pcs) 8 img
Resolution Test
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("Different_Resolution_on_my_UMAP-0.1-to-1.Robj") All_samples_Merged An object of class Seurat 63098 features across 49193 samples within 3 assays Active assay: SCT (26469 features, 3000 variable ...
5052 sym Python (3418 sym/15 pcs) 9 img
Resolution Test
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("Different_Resolution_on_my_UMAP-0.3-to-2.Robj") All_samples_Merged An object of class Seurat 63098 features across 49193 samples within 3 assays Active assay: SCT (26469 features, 3000 variable ...
2954 sym Python (1848 sym/11 pcs) 9 img
Document
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("../SS_Escape_final-c2.Robj") 3. Escape # # 1: Molecular Signture Database # GS.hallmark <- getGeneSets( # species = "Homo sapiens", # libra...
10642 sym Python (6964 sym/24 pcs) 17 img
Document
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...
29911 sym R (18719 sym/72 pcs) 51 img