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nmabbasi

NASIR MAHMOOD ABBASI

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Enrichment after FC Scanner Analysis
DE with FC Scanner
Tables of celllines based on clusters harmony0.9
Tables of celltypes based on cell_lines
Tables of celltypes based on clusters harmony0.9
Cell_lines vs PBMC
Patients vs PBMC-Tcells
P1,P2,P3
TCR Analysis using harmony integrated UMAP
TCR Analysis using harmony integrated UMAP
Cell Line derived from each patient DE comparison-part2
Top10 categories
Significant genes for strings
0.05 2 -2
Sézary Syndrome Cell Line derived from each patient DE comparison
Cell lines derived from patient
SCpubr
Sézary Syndrome SCpubr Visualization
https://enblacar.github.io/SCpubr-book-v1/04-FeaturePlots.html
Sézary Syndrome Cell Line Top5 gene markers
Top5 and Top10
Sézary Syndrome top10 Clusters
Differential Expression Analysis of SS vs PBMC10X+PBMC
based on CSV file
DE_Harmony_integrated_0.9_SS vs PBMC10X+PBMC_Tcells
Differential Expression Analysis
1vs2 6vs16
InferCNV Analysis
Percentage of cells CNVs
Harmony_Intergrations_and_visualization_of_PBMC-10x.
Its juts to visualize cluster, clustree and tables
Harmony integrations of PBMC10x by sample_group-theta-0.5
Theta-0.5
Harmony integrations of PBMC10x by cell_line_group-theta-0.5
Theta-0.5
Harmony integrations of PBMC10x by cell_line-theta-0.5
Theta-0.5
Harmony integrations of PBMC10x by cell_line-theta-0
Theta-0
Harmony integrations of PBMC10x by cell_line-theta-Default
Theta-Default
Sézary Syndrome Cell Line Analysis-DE-Integrated
DE integrated
Sézary Syndrome Cell Line Analysis-DE-PBMC10X
DE Merged with PBMC10x
Differential Expression Analysis of SS vs PBMC10X+PBMC
based it on clusters after harmony integration which I did
Harmony integrations of PBMC10x-part4
final version to Discuss
Multiple Harmony integrations of PBMC10x-part3
on HPC we use sample group, cell line group and cell line
Harmony integrations of PBMC10x bu sample group, cell line group and cell line
Multiple Harmony integrations of PBMC10x
1:22 Different methods of harmony are tried.
Harmony Integration of PBMC10x-part2
1:22 0.5
Harmony Integration of PBMC10x-Part1
1:22 0.5
RPCA-CCA-Harmony Integration of PBMC10x with NormalizeData-VST on samples part3
Its on Rserver 1:20 1.2
Harmony Integration of PBMC10x with SCT on samples part2
Merged All samples with PBMC_10x and apply SCT on 1:22
Object is saved as All_Samples_Merged_with_10x_Azitmuth_Annotated_SCT_HPC_without_harmony_integration.robj
Harmony Integration of PBMC10x with SCT on samples
old method of normalizing the SCT clusters
Merged All samples with PBMC_10x
1:12 PC
Merged All samples with PBMC_10x
First regressed in SCT for cell_line and then we used harmony
Merged All samples with PBMC_10x
HPC 1:22
Merged All samples with PBMC_10x_on_HPC
SCT normalization of merged samples and Harmony Integration
PBMC10X included
Merged All samples with PBMC_10x and SCT analysis on annotated Object
Did analysis on Rstudio server
Merging all our cell lines and controls(PBMC-PBMC10x) into single seurat object-Robj
Merging all our cell lines and controls(PBMC-PBMC10x) into single seurat object-Robj
PBMC_10x
New Reference
Cytogenetic Analysis
Comparison of inferCNV with Cytogenetics data
Sézary Syndrome Cell Line DE Analysis
Phylogeny_based on inferCNV
Phylogeny_based on RNA Expression-euclidean_pearson
Differential Expression Analysis at 0.9
WNN analysis of CITE-seq, RNA + ADT-Part2
Inference and analysis of cell-cell communication using CellChat-SS_cellLines
SS Object is USED
TCR Analysis-Part2
New UMAP
WNN analysis of CITE-seq, RNA + ADT-PART5
res:0.4
WNN analysis of CITE-seq, RNA + ADT_part4
WNN analysis of CITE-seq, RNA + ADT_part3
Res=0.9 dims.list = list(1:20, 1:18), modality.weight.name = "RNA.weight"
WNN analysis of CITE-seq, RNA + ADT part2
dims.list = list(1:20, 1:18), modality.weight.name = "RNA.weight"
WNN analysis of CITE-seq, RNA + ADT
Inference and analysis of cell-cell communication using CellChat-Melange
Melange
UMAP of T cells without other PBMC cells using clusters and PC-1:20
UMAP of T cells without other PBMC cells using clusters and PC-1:20
L1_Merged_first_HPC_PC-1:21-6-old_script
L1_Merged_first_HPC_PC-1:21-6-old_script
L1_Merged_first_HPC_PC-1:50-5
L1_Merged_first_HPC_PC-1:50-5
L1_Merged_first_HPC_PC-1:50-4
L1_Merged_first_HPC_PC-1:50-4
L1_Merged_first_HPC_PC-1:50-3
L1_Merged_first_HPC_PC-1:50-3
UMAP of T cells-PC-1:50-2
Old Script used
Just T cells Analysis_PC-1:50
UMAP of T cells without other PBMC cells using clusters and PC-1:50
L7
Cell Line L7 Analysis
L6
Cell Line L6 Analysis
L5
Cell Line L5 Analysis
L3
Cell Line L3 Analysis
L4
Cell Line L4 Analysis
L4_notebook
Cell Line L4 Analysis
L3_Notebook
Cell Line L3 Analysis
L2_Notebook
Cell Line L2 Analysis
L2
Cell Line L2 Analysis
L1_notebook
Cell Line L1 Analysis
L1
Cell Line L1 Analysis
cell-cell communication using CellChat
Inference and analysis of cell-cell communication using CellChat
Document-Harmony-Integration
1:13 0.1-1.2
Document-Harmony
Integration by Harmony_on_logNormalization
1:17 0.5
Integration by Harmony_on_SCTransform_DATA
Same parameters Without findNeigbors and FindClusters
1-Harmony Integration_on_SCTransform
Its done on SCTransform data with 1:13 PCA 0.5 Res
Integration by Harmony_by_K_1-12
1:12
Integration by Harmony_by_K_1-30
0.5
Integration by Harmony_by_K_1-50
1:50 0.5
Integration by Harmony_by_K
1;20 0.5
Integration by CCA_by_K_1-12
used K code 1:20 log Norm 1:12 integration
Integration by CCA_by_K_1-20
used K code 1:20 log Norm 1:20 integration
Integration by CCA_by_K
used K code 1:20 log Norm 1:50 integration
Harmony Integration_Test3
Harmony Integration_Test2
Harmony Integration_Test1
PCA TEST and Harmony
CCA_harmony_0.5
dims: 1:15
CCA-Harmony_new
rpca-Harmony_new
Integration-Harmony
Integration-CCA
rpca-Integration
Corrected-UMAP
integration by Different Methods-rpca-CCA-Harmony
ADT Normalization
UMAP-0.7 with Annotation
Resolution Test
0.3-2
Resolution Test
Document
Escape Visualization
Document
Analysis of TCR-SS