cobeylab / psc_repertoire

Analysis of B cell repertoires from patients with primary sclerosing cholangitis (PSC). Collaboration led by Dustin Shaw and Bana Jabri

psc_repertoire

Code for the B cell repertoire analysis in Shaw et al. (2021), Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis.

Dependencies

mafft v7.310

partis v0.15.0

IgPhyML v1.1.0 (part of the Immcantation suite)

R v3.6.1 with packages dplyr, tidyr, readr, seqinr, stringr, ggplot2, cowplot, forcats, yaml, msa, Biostrings.

python 2.7.15 with packages Bio, itertools, re, numpy, glob.