Immune-repertoire-network

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)

upstream

the upstream is shared by all projects using this pipeline

VDJ assignement, cdr3 extraction

the main script is upstream.py

downstrean

network analysis

network generation based on vj, cdr3

the main script is network_bcr.sh, parameters are in config.json

others

Other softwares or programs might be used in further analysis. Check individual paper for details.