Code for analyses of 10x single-cell data used in Montiel-Armendariz et al. 2026, "B cell αv integrin regulates tissue specialization and clonal expansion of lung germinal center and memory B cells after viral infection".
The code is organized as three scripts:
- Integrin_B_cell_10x_analysis_pre_ChangeO.Rmd - Rmarkdown file including code for loading 10x data, performing quality control and cell filtering, projection, clustering, and analyses of cell numbers and phenotypes across tissues, mouse genotypes, and antigen specificities.
- Integrin_B_cell_10x_runChangeO.sh - Shell script including commands for running Immcantation tools on single-cell BCR sequence data to determine V/J genes, and infer germline sequences, clonal lineages, and somatic hypermutation.
- Integrin_B_cell_10x_analysis_post_ChangeO.Rmd - Rmarkdown file including code for combined analysis of the 10x gene expression data and the Immcantation-processed BCR sequence data.