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  1. CD4bs-mAb-Infusion CD4bs-mAb-Infusion Public

    Contains scripts and data used for data analysis in Thomas et al., 2024 (doi: 10.1016/j.isci.2024.109495)

    R

  2. BCR-phylogenetic-networks BCR-phylogenetic-networks Public

    Script to perform evolutionary analysis of MBC subsets via BCR sequences

    R

  3. VDJ-AA-Kmer-Similarity VDJ-AA-Kmer-Similarity Public

    Scripts to perform pairwise comparison of VDJ kmer sequences using various metrics

    Python

  4. TIL-analysis TIL-analysis Public

    Repo for analysis of TIL repertoires in sequential tumour passages across mouse strains (CTVT project)

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  5. ALICE-HPC-wrapper ALICE-HPC-wrapper Public

    Repository for an HPC implementation of the ALICE pipeline for identifying statistically enriched TCRs from single timepoint bulk sequencing data

    Shell

  6. tracer-to-immcantation tracer-to-immcantation Public

    Repository for reconstructing TCRs and subsequently running through ChangeO/IgBLAST for identification of CDR3 sequences

    Shell