Publications by Nasir Mahmood Abbasi
Harmony integrations of PBMC10x by Patient -theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../22-Seurat_Integrate/0-R_Objects/CD4Tcells_SCTnormalized_done_on_HPC_inluding_Patient_origin.robj") # Visualize before Harmony integration DimPlot(All_samples_Merged, reduction = "umap", group.by...
14051 sym Python (19790 sym/42 pcs) 16 img
Harmony integrations of PBMC10x by Patient and orig.ident-theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../22-Seurat_Integrate/0-R_Objects/CD4Tcells_SCTnormalized_done_on_HPC_inluding_Patient_origin.robj") # Visualize before Harmony integration DimPlot(All_samples_Merged, reduction = "umap", group.by...
14095 sym Python (19579 sym/42 pcs) 16 img
Harmony integrations of PBMC10x by cellLine -theta-default both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../22-Seurat_Integrate/0-R_Objects/CD4Tcells_SCTnormalized_done_on_HPC_inluding_Patient_origin.robj") # Visualize before Harmony integration DimPlot(All_samples_Merged, reduction = "umap", group.by...
13987 sym Python (19506 sym/42 pcs) 16 img
Harmony integrations of PBMC10x by cell_line-theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../22-Seurat_Integrate/0-R_Objects/CD4Tcells_SCTnormalized_done_on_HPC_inluding_Patient_origin.robj") # Visualize before Harmony integration DimPlot(All_samples_Merged, reduction = "umap", group.by...
14063 sym Python (19845 sym/42 pcs) 16 img
RPCA-Integration of PBMC10x with SCT on samples part1
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("0-R_Objects/SS_CD4_Tcells_Azimuth_Annotated_PBMC10x_final_for_SCT_and_Integration.robj") All_samples_Merged <- filtered_seurat All_samples_Merged An object of class Seurat 36752 features across 49372 samples within 5 as...
23973 sym R (29066 sym/134 pcs) 18 img
RPCA-CCA-Harmony Integration of PBMC10x with SCT on samples part1.2
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("0-R_Objects/SS_CD4_Tcells_Azimuth_Annotated_PBMC10x_final_for_SCT_and_Integration.robj") All_samples_Merged <- filtered_seurat All_samples_Merged An object of class Seurat 36752 features across 49372 samples within 5 as...
23973 sym R (29066 sym/134 pcs) 18 img
RPCA--Harmony Integration of PBMC10x with SCT on samples part2
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("0-R_Objects/SS_CD4_Tcells_Azimuth_Annotated_PBMC10x_final_for_SCT_and_Integration.robj") All_samples_Merged <- filtered_seurat All_samples_Merged An object of class Seurat 36752 features across 49372 samples within 5 as...
23680 sym R (15737 sym/55 pcs) 28 img
Different evaluation test on harmony integration on patient origin and cell_line-theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../0-R_Objects/CD4Tcells_harmony_integrated_0.5_theta_patientorigin_cell_line.Robj") 3. Harmony Visualization DimPlot(All_samples_Merged, reduction = "umap", group.by = "cell_line", ...
6764 sym R (23004 sym/47 pcs) 16 img
Harmony integrations of PBMC10x by patient origin and cell_line-theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../0-R_Objects/CD4Tcells_SCTnormalized_done_on_HPC_inluding_Patient_origin.robj") # Visualize before Harmony integration DimPlot(All_samples_Merged, reduction = "umap", group.by = "Patient_origin",...
14091 sym Python (19842 sym/42 pcs) 16 img
Different evaluation test on harmony integration on patient origin and cell_line-theta-0.5 both
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control after filtration load("../0-R_Objects/CD4Tcells_harmony_integrated_0.5_theta_patientorigin_cell_line.Robj") 3. Harmony Visualization DimPlot(All_samples_Merged, reduction = "umap", group.by = "cell_line", ...
4721 sym Python (2733 sym/16 pcs) 15 img