TCR Read Extraction and Cytokine Analysis for plate-based single T cell receptor sequencing generated by a protocol originally described in Han et al., Nature Biotechnology 2014.
This repository provides capabilities for extraction of TCR sequences and cytokine / transcription factor data based on IMGT, CD-HIT, MUSCLE, and BLAST.
This pipeline has been used in the following publications:
Penter et al., EJI 2018
Penter et al., Oncoimmunology 2019
Lammoglia Cobo et al., Cytotherapy 2022
Welters et al., Cancer Immunology Research 2022