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Codes from the paper "Heterotypic CD8 T cell clusters isolated from clinical samples are distinct and enriched for antitumor activity"

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PeeperLab/HeterotypicClustersR

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ec29209 · Dec 20, 2024

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HeterotypicClustersR (Latest Updates:2024-12-20)

This repository contains the scripts related to the analysis of scRNA seq and scTCR seq from the clusters datasets. My Image

Dependencies

R > 4.3.1
Seurat == 4.4.0
Harmony == 1.2.1
AUCell == 1.24.1
scRepertoire == 2.0.4
Nichenet == 2.2.0

Overview

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

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Codes from the paper "Heterotypic CD8 T cell clusters isolated from clinical samples are distinct and enriched for antitumor activity"

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