About
TRIBAL¶
TRIBAL (TRee Inference of B cell clonAl Lineages) is a method to infer B cell lineage trees from single-cell RNA sequencing data. TRIBAL trees jointly model the evolutionary processes of somatic hypermutation and class switch recombination.
The input to TRIBAL is a multiple sequence alignment for each of the predetermined clonotypes aligned to the germline sequence and the isotype of each sequenced B cell. The output is forest of B cell lineage trees, one for each clonotype, with nodes labeled by BCR sequences (concatenated heavy and light chain) and the isotype of each B cell, as well as an isotype transition probability matrix.
Contact¶
TRIBAL is a collaboration between the El-Kebir Lab at UIUC and the Laboratory for Computational Immunology at the University of Chicago. For help and questions please contact Mohammed El-Kebir and Aly A. Khan.
Dependencies¶
Depends: dnapars, mafft, glpk
Imports: networkx, pyomo, numpy, pandas, ete3, Bio, pygrahpviz
Authors¶
Leah L. Weber
Derek Reiman
Mrinomy S. Roddur
Yuanyuan Qi
Mohammed El-Kebir
Aly A. Khan
Citing¶
To cite TRIBAL in publications, please use
Weber, L. L., Reiman, D., Roddur, M. S., Qi, Y., El-Kebir, M., & Khan, A. A. TRIBAL: Tree Inference of B cell Clonal Lineages. bioRxiv. doi.org/10.1101/2023.11.27.568874.