Dynamic spectrum of ectopic lymphoid B cell activation in the RA synovium characterized by NR4A nuclear receptor expression

Preprint is here

Organization and use

synovium_sc

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

reanalysis

Code to infer cell types on external data sets e.g. figure 1E. Uses R 3.6.1

amp_bulk

differential expression of NR4A in low-input bulk data, e.g. figure 1F. Uses R 4.1.

Data

Raw data from the 10X run in this manuscript is on GEO. Most the batteries are included to run these analysis here.

Exceptions: AMP data for the amp_bulk and reanalysis workflows will need to be downloaded from IMMPort 1, 2 and/or GEO, since we did not have permission to directly (re)-share.

R packages

To install necessary packages to reproduce an analysis, change to a subdirectories, and run:

install.packages('renv')
renv::restore()

You will need to be running the same version of R as used when the renv lockfiles were written...