## Recently Published

##### 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

##### 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

##### 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

##### 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

##### TCR Analysis-Part2

New UMAP

##### 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"

##### 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

##### 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_1-50

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

##### CCA_harmony_0.5

dims: 1:15

##### Resolution Test

0.3-2

##### Document

Escape Visualization

##### Document

Analysis of TCR-SS