Papers using this pipeline:
Longitudinally persistent cerebrospinal fluid B cells can resist treatment in multiple sclerosis AL Greenfield, R Dandekar, A Ramesh, EL Eggers, H Wu, S Laurent, ... JCI insight 4 (6)
Clonal relationships of CSF B cells in treatment-naive multiple sclerosis patients EL Eggers, BA Michel, H Wu, S Wang, CJ Bevan, A Abounasr, NS Pierson, ... JCI insight 2 (22)
Effect of ocrelizumab on B- and T-cell immune repertoires in patients with relapsing MS (in submission)
VDJ assignement, cdr3 extraction
the main script is upstream.py
network generation based on vj, cdr3
the main script is network_bcr.sh, parameters are in config.json
Other softwares or programs might be used in further analysis. Check individual paper for details.