This repository contains the scripts related to the analysis of scRNA seq and scTCR seq from the clusters datasets.
R > 4.3.1
Seurat == 4.4.0
Harmony == 1.2.1
AUCell == 1.24.1
scRepertoire == 2.0.4
Nichenet == 2.2.0
The Scripts contains following analysis:
1. Main - Workflow for processing cell ranger outputs of aligned sequencing samples and integrating samples for cell types identification.
2. Plots - celltype specific analysis
3. Signatures - cluster signature analysis
4. Nichenet - cell-cell interactions analysis among clusters groups
5. Reactivity - Tcell reactivity analysis
6. Stats - clusters enrichment statistics
7. TCR_activity - TCR activity comparison between clusters and singlets
8. Tumor_Analysis - Tumor cluster enrichment analysis
9. Infer_CNV - Inferred copy number analysis of tumor cells
10. Response - Cluster signature distribution analysis in Barras response data