Publications by Nasir Mahmood Abbasi

PseudoBulk_P2_vs_P3

19.03.2025

1. load libraries 2. load seurat object #Load Seurat Object load("/home/bioinfo/23-Harmony_Integration/0-robj/5-Harmony_Integrated_All_samples_Merged_CD4Tcells_final_Resolution_Selected_0.8_ADT_Normalized_cleaned_mt.robj") pseudobulk_seurat <- All_samples_Merged # Set the label column with "P1", "P2", "P3", and "Control" pseudobulk_seurat$label...

30776 sym R (23307 sym/62 pcs) 12 img

PseudoBulk_P1_vs_P2

18.03.2025

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") # # pseudobulk_seurat <- All_samples_Merged # # # Set the label column with "P1", ...

30921 sym R (23190 sym/49 pcs) 14 img

PseudoBulk Analysis using Libra_filtred_Mean

18.03.2025

1. load libraries 2. load seurat object pseudobulk_seurat <- All_samples_Merged # Assign labels and ensure 'Control' is the reference pseudobulk_seurat$label <- factor( ifelse(pseudobulk_seurat$orig.ident %in% c("PBMC", "PBMC10x"), "Control", "Malignant"), levels = c("Malignant", "Control") ) # Double-check the referenc...

28826 sym R (21613 sym/53 pcs) 15 img

Signature Markers(Malignat_vs_Normal_CD4Tcells) Top30up,down

18.03.2025

1. load libraries 2. Load the filtered upregulated and Downregulated genes 3. Initial test df <- df[!(df$Malignant.exp < 0.20 & df$Control.exp < 0.20), ] df <- as.data.frame(df) write.csv(df, "../18-03-25_top-markers/Psedibulk_Deseq2_filtered_on_mean.csv", row.names = FALSE) # Ensure the dataframe has necessary columns: "gene", "avg_logFC", "...

11104 sym R (6750 sym/17 pcs) 13 img

PseudoBulk Analysis using Libra RNA assay-Deseq2-LRT

17.03.2025

1. load libraries 2. load seurat object pseudobulk_seurat <- All_samples_Merged # Assign labels and ensure 'Control' is the reference pseudobulk_seurat$label <- factor( ifelse(pseudobulk_seurat$orig.ident %in% c("PBMC", "PBMC10x"), "Control", "Malignant"), levels = c("Malignant", "Control") ) # Double-check the referenc...

28520 sym R (21537 sym/54 pcs) 12 img

PseudoBulk Analysis using Libra RNA assay-Deseq2-LRT-Final-P1

17.03.2025

1. load libraries 2. load seurat object pseudobulk_seurat <- All_samples_Merged # Assign labels and ensure 'Control' is the reference pseudobulk_seurat$label <- factor( ifelse(pseudobulk_seurat$orig.ident %in% c("PBMC", "PBMC10x"), "Control", "Malignant"), levels = c("Malignant", "Control") ) # Double-check the referenc...

39295 sym R (33138 sym/76 pcs) 22 img

PseudoBulk Analysis using Libra RNA assay-Deseq2-LRT

17.03.2025

1. load libraries 2. load seurat object #Load Seurat Object L7 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") pseudobulk_seurat <- All_samples_Merged pseudobulk_seurat$label <- factor( ifelse(...

39208 sym R (29936 sym/61 pcs) 22 img

PseudoBulk Analysis using Libra RNA assay-edgeR-LRT

16.03.2025

1. load libraries 2. load seurat object #Load Seurat Object L7 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") pseudobulk_seurat <- All_samples_Merged pseudobulk_seurat$label <- factor( ifelse(...

39574 sym R (30538 sym/63 pcs) 22 img

PseudoBulk Analysis_good_script

14.03.2025

1. load libraries 2. load seurat object #Load Seurat Object L7 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") pseudobulk_seurat <- All_samples_Merged pseudobulk_seurat$label <- factor( ifelse(...

35177 sym R (23514 sym/55 pcs) 17 img

PseudoBulk Analysis

14.03.2025

1. load libraries 2. load seurat object 3. DE using LIBRA libra_result = run_de(pseudobulk_seurat, de_family = 'pseudobulk', de_method = 'DESeq2', de_type = 'LRT') Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array of at least two dimensions LS0tCnRpdGxlOiAiUHNldWRvQnVsayBBbmFseXNpcyIKYXV0aG9yOiBOYXNpciBNYWhtb...

2699 sym