Publications by Nasir Mahmood Abbasi
Trajectory inference using Slingshot
1. load libraries 2. Nice function to easily draw a graph: 3. Reading data load("../2025_NewHarmony_Integrated_Files/0-imp_Robj/0-robj/5-Harmony_Integrated_All_samples_Merged_CD4Tcells_final_Resolution_Selected_0.8_ADT_Normalized_cleaned_mt.robj") # Define some color palette pal <- c(scales::hue_pal()(8), RColorBrewer::brewer.pal(9, "Set1"), RCo...
13301 sym 10 img
inferCNV analysis
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../../To_Transfer_between_computers/23-Harmony_Integration/0-robj/5-Harmony_Integrated_All_samples_Merged_CD4Tcells_final_Resolution_Selected_0.8_ADT_Normalized_cleaned_mt.robj") infercnv_object <- readRDS("inferCNV_An...
3465 sym R (1861 sym/3 pcs)
TF Activity inference analysis
1. load libraries library(dplyr) Attachement du package : ‘dplyr’ Les objets suivants sont masqués depuis ‘package:stats’: filter, lag Les objets suivants sont masqués depuis ‘package:base’: intersect, setdiff, setequal, union library(Seurat) Registered S3 method overwritten by 'htmlwidgets': method from ...
5026 sym R (6445 sym/37 pcs) 6 img
NK Proliferating vs Control_filtred_on_mean
1. load libraries library(dplyr) Attachement du package : ‘dplyr’ Les objets suivants sont masqués depuis ‘package:stats’: filter, lag Les objets suivants sont masqués depuis ‘package:base’: intersect, setdiff, setequal, union library(Seurat) Le chargement a nécessité le package : SeuratObject Le chargement a nécessit�...
4820 sym R (5532 sym/38 pcs) 14 img
Azimuth Annotation Report
1. load libraries library(dplyr) Attachement du package : ‘dplyr’ Les objets suivants sont masqués depuis ‘package:stats’: filter, lag Les objets suivants sont masqués depuis ‘package:base’: intersect, setdiff, setequal, union library(Seurat) Le chargement a nécessité le package : SeuratObject Le chargement a nécessit�...
4768 sym R (5532 sym/38 pcs) 14 img
HSPC vs Control_filtred_on_mean
1. load libraries 2. Load the filtered list on mean expression # Load the DE results from CSV HSPC_vs_Control <- read.csv("3-RNA_HSPC_vs_Control_Filtered_by_MeanExp.csv", stringsAsFactors = FALSE) 3. Volcano Plots library(dplyr) library(EnhancedVolcano) # Assuming you have a data frame named HSPC_vs_Control # Filter genes based on lowest p-va...
18021 sym R (15088 sym/42 pcs) 9 img
plot1cell a package for advanced single cell data visualization
1. load libraries library(dplyr) library(Seurat) library(ComplexHeatmap) # https://github.com/immunogenomics/presto library(presto) library(tictoc) library(plot1cell) 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../../To_Transfer_between_computers/23-Harmony_Integration/0-robj/5-Harm...
11611 sym R (11267 sym/44 pcs) 6 img
Wilcox Analysis RNA Top Markers2
1. load libraries 2. load seurat object #Load Seurat Object load("/home/nabbasi/isilon/To_Transfer_between_computers/23-Harmony_Integration/0-robj/5-Harmony_Integrated_All_samples_Merged_CD4Tcells_final_Resolution_Selected_0.8_ADT_Normalized_cleaned_mt.robj") Layers(All_samples_Merged@assays$RNA) [1] "data" "counts" 3. clusters vs the rest mar...
13628 sym R (7132 sym/22 pcs) 3 img
Wilcox Analysis RNA Top Markers
1. load libraries 2. load seurat object #Load Seurat Object load("/home/nabbasi/isilon/To_Transfer_between_computers/23-Harmony_Integration/0-robj/5-Harmony_Integrated_All_samples_Merged_CD4Tcells_final_Resolution_Selected_0.8_ADT_Normalized_cleaned_mt.robj") Layers(All_samples_Merged@assays$RNA) [1] "data" "counts" 3. clusters vs the rest De...
7996 sym R (4712 sym/29 pcs) 8 img
NK Proliferating vs Control_filtred_on_mean
1. load libraries 2. Load the filtered list on mean expression # Load the DE results from CSV df <- read.csv("3-RNA_NK_Prolif_vs_Control_Filtered_by_MeanExp.csv", stringsAsFactors = FALSE) DE_results_df <- df 3. Volcano Plots library(dplyr) library(EnhancedVolcano) # Assuming you have a data frame named Malignant_CD4Tcells_vs_Normal_CD4Tcells...
18352 sym R (13777 sym/30 pcs) 8 img