Flexible distance measures for comparing T cell receptors
tcrdist3 is a python API-enabled toolkit for analyzing T-cell receptor repertoires. Some of the functionality and code is adapted from the original tcr-dist package which was released with the publication of Dash et al. Nature (2017) doi:10.1038/nature22383. This package contains a new API for computing tcrdistance measures as well as new features for biomarker development (bioRxiv (2020)). The package has been expanded to include gamma-delta TCRs; it has also been recoded to increase CPU efficiency using numba, a high-performance just-in-time compiler.
pip install tcrdist3
or
pip install git+https://github.com/kmayerb/tcrdist3.git@0.1.9
docker pull quay.io/kmayerb/tcrdist3:0.1.9
More documentation can be found at tcrdist3.readthedocs.
import pandas as pd
from tcrdist.repertoire import TCRrep
df = pd.read_csv("dash.csv")
tr = TCRrep(cell_df = df,
organism = 'mouse',
chains = ['alpha','beta'],
db_file = 'alphabeta_gammadelta_db.tsv')
tr.pw_alpha
tr.pw_beta
tr.pw_cdr3_a_aa
tr.pw_cdr3_b_aaTCR meta-clonotypes for biomarker discovery with tcrdist3: quantification of public, HLA-restricted TCR biomarkers of SARS-CoV-2 infection
Mayer-Blackwell K, Schattgen S, Cohen-Lavi L, Crawford JC, Souquette A, Gaevert JA, Hertz T, Thomas PG, Bradley PH, Fiore-Gartland A. bioRxiv (2020).
Pradyot Dash, Andrew J. Fiore-Gartland, Tomer Hertz, George C. Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E. Bridie Clemens, Thi H. O. Nguyen, Katherine Kedzierska, Nicole L. La Gruta, Philip Bradley & Paul G. Thomas Nature (2017).