Human memory CD4+ T-cells recognize Mycobacterium tuberculosis-infected macrophages amid broader pathogen-specific responses.

The script consists of the followings parts:

I. Preintegration processing

1. Preparing the session
2. Loading data sets and transforming them into Seurat objects
3. Adjusting the meta.data structure
4. Adding cell barcodes to TCR read tables
5. Quantify percentages of mitochondrial, ribosomal, TCR genes
6. Quality control: removal low quality cells
7. Cell cycle scoring
8. Combining scRNA- and scTCR-seq data data
9. Labeling of clonally expanded cells
10. Merging samples
11. Variance stabilization

II. Sample integration/Batch correction

III. Postintegration analysis

1. Cell clustering
2. Quality control: removal of monocytic contamination
3. Gene expression analysis
4. Assessment of clonal expansion
5. Single-cell trajectory analysis
6. Mapping CDR3 motifs on the UMAP
7. Differential gene expression analysis
8. Biological theme comparison/Reactome pathway overrepresentation analysis
9. Cell-cell communication analysis