CD4_CD8-Manuscript

This is the Github repository associated with Carter et al. (2019) "Single T cell sequencing demonstrates the functional role of αβ TCR pairing in cell lineage and antigen specificity" Front. Immunol. doi: 10.3389/fimmu.2019.01516

Data

Paired $\alpha\beta$ TCR sequences, as well as V(D)J annotations, are provided as pickled Pandas dataframes within the "Data" folder. The AbVitro TCR sequences for Subjects 1-5 were obtained from Grigaityte et al. (bioRxiv 213462). TCR sequences obtained in this study using the 10x Genomics platofrm (for Subjects 1,3,5,6) are provided in these dataframes. We additionally provide the VDJdb (https://vdjdb.cdr3.net) antigen specificity annotations that were used to generate Figure 5.

Analysis

iPython notebooks are provided for each of the main figures in the Scripts folder.

Dependencies: Python 3.6, numpy 1.12.1, matplotlib 2.1.1, seaborn 0.8.1, scipy 1.0.0, sklearn 0.19.1, pandas 0.22.0, statsmodels 0.8.0, xgboost 0.81, qvalue (https://github.com/nfusi/qvalue)