Publications by Nasir Mahmood Abbasi
Differential Expression Analysis - Filtering and Visualization
1. Load Libraries 2. Load Data 2.1 Load CSV Files with Mean Expression # Load the CSV files with mean expression data markers_mast_batch <- read.csv("0-imp_Robj/1-MAST_with_batch_as_Covariate_with_meanExpression.csv", row.names = 1) markers_wilcox <- read.csv("0-imp_Robj/2-Wilcox_min.pct_logfcT-0_with_meanExpression.csv", row.names = 1) markers_m...
7507 sym 4 img
Merged All samples with PBMC_10x, Removed non CD4 T cells from Control, Apply_SCT_then_Harmony_theta-0.5
1. load libraries Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t ── Installed datasets ──────────────────────────────── SeuratData v0.2.2.9001 ── ✔ ...
21176 sym R (30196 sym/111 pcs) 30 img
Differential Expression Analysis using Harmony Integrated Clusters
1. Load Libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("0-imp_Robj/Harmony_integrated_CD4Tcells_harmony_integrated.Robj") All_samples_Merged An object of class Seurat 62926 features across 49360 samples within 6 assays Active assay: SCT (26174 features, 3000 variable featur...
10760 sym R (82308 sym/39 pcs) 5 img
Differential Expression Analysis using Harmony Integrated Clusters
1. Load Libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("0-imp_Robj/Harmony_integrated_CD4Tcells_harmony_integrated.Robj") All_samples_Merged An object of class Seurat 62926 features across 49360 samples within 6 assays Active assay: SCT (26174 features, 3000 variable featur...
11680 sym R (82998 sym/39 pcs) 5 img
Differential Expression Analysis - Filtering and Visualization
1. Load Libraries 2. Load Data 2.1 Load CSV Files with Mean Expression # Load the CSV files with mean expression data markers_mast_batch <- read.csv("0-imp_Robj/TEST_MAST_with_batch_results1_with_meanExpression.csv", row.names = 1) markers_wilcox <- read.csv("0-imp_Robj/TEST_Wilcox_without_batch_results2_with_meanExpression.csv", row.names = 1) m...
7542 sym 4 img
Differential Expression Analysis - Filtering and Visualization
1. Load Libraries 2. Load Data 2.1 Load CSV Files with Mean Expression # Load the CSV files with mean expression data markers_mast_batch <- read.csv("0-imp_Robj/TEST_MAST_with_batch_results1_with_meanExpression.csv", row.names = 1) markers_wilcox <- read.csv("0-imp_Robj/TEST_Wilcox_without_batch_results2_with_meanExpression.csv", row.names = 1) m...
7542 sym 4 img
Merged All samples with PBMC_10x and removed non CD4 T cells from Control and B cells from L4 and regress nCountRNA and apply SCT_finalized
1. load libraries Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t ── Installed datasets ──────────────────────────────── SeuratData v0.2.2.9001 ── ✔ ...
24781 sym R (36413 sym/174 pcs) 36 img
Harmony integrations of PBMC10x by cell_line-theta-0.5_removing non CD4Tcells and B cells from L4_also_ILC_NK_CD14_Mono
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("0-imp_Robj/All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration_removed_nonCD4cells_from_control_and_Bcells_from_L4_ILC_NK_CD14Mono_no_nCount_nFeatureRegress_ready_for_Harmony_final.robj") # Displa...
19272 sym Python (23545 sym/43 pcs) 14 img
Seurat Integration of PBMC10x-Rserver-rpca-part1
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("0-OBJ/CD4Tcells_no_B_cells_in_L4_SCT_Ready_for_integration.robj") All_samples_Merged An object of class Seurat 62931 features across 49388 samples within 6 assays Active assay: SCT (26179 featur...
10909 sym Python (42218 sym/120 pcs) 11 img
Seurat Integration of PBMC10x-HPC-rpca
1. load libraries library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t library(SeuratObject) library(SeuratData) ── Installed datasets ────────────────────────�...
4672 sym R (12818 sym/257 pcs) 3 img