Publications by Nasir Mahmood Abbasi
Integration by Harmony_by_K
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, data 4 other assays...
4990 sym 6 img
Integration by Harmony_by_K_1-50
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, data 4 other assays...
5005 sym Python (4610 sym/15 pcs) 6 img
Integration by Harmony_by_K_1-30
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, data 4 other assays...
5005 sym Python (4610 sym/15 pcs) 6 img
Integration by Harmony_by_K_1-12
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, data 4 other assays...
5005 sym Python (4611 sym/15 pcs) 6 img
Integration by CCA_by_K_1-12
1. load libraries 2. Load Seurat Object # load("AllSample_corrected_AzimuthAnnotated_L1.Robj") # merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 2000 variable features) 3 layers present: counts, data, scale.dat...
6837 sym Python (5567 sym/15 pcs) 10 img
Integration by CCA_by_K_1-20
1. load libraries 2. Load Seurat Object # load("AllSample_corrected_AzimuthAnnotated_L1.Robj") # merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 2000 variable features) 3 layers present: counts, data, scale.dat...
6837 sym Python (5567 sym/15 pcs) 10 img
Integration by CCA_by_K
1. load libraries 2. Load Seurat Object # load("AllSample_corrected_AzimuthAnnotated_L1.Robj") # merged_seurat_filtered <- All_samples_Merged merged_seurat_filtered An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 2000 variable features) 3 layers present: counts, data, scale.dat...
6827 sym Python (4546 sym/13 pcs) 10 img
Harmony Integration_Test2
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_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 assays Active assay...
6518 sym Python (4419 sym/25 pcs) 17 img
Harmony Integration_Test3
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_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 assays Active assay...
7349 sym Python (5129 sym/24 pcs) 17 img
PCA TEST and Harmony
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_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 assays Active assay...
16392 sym R (11235 sym/37 pcs) 17 img