Code and primary data for expression and BCR for single cells from peripheral blood and synovium from RA134, RA172, RA195, RA221, e.g. figure 1A-1D, 2A-2D. Uses R 3.5.1
02vdj_explore.Rmd Filter and QC of VDJ data 03cluster_cdr3.Rmd Clonotype definitions, etc of VDJ data. 04expression_cluster_de.Rmd Unsupervised clustering and differential expression using Seurat. Also some analysis connecting VDJ props to clustering. 05slingshot.Rmd Trajectory analysis using slingshot. 06rep_and_expression.Rmd Further analysis of clonotype properties (e.g. permutation tests) compared to gene expression defined subpopulations defined in 04expression_cluster_de.md.