Tools and Resources
Here are links to some of the tools and resources I’ve made for various tasks in TCR research.
| Tool / Resource | Purpose |
|---|---|
stitchr | Generate full-length coding TCR sequences from V/J/CDR3 classifiers, for functional validation or high-throughput modelling. |
autoDCR | Flexible V/J/CDR3 annotation from deep sequencing data. A custom fork of the Chain lab’s Decombinator tool, that matches tags along the entire length of TCR variable domains, allowing full allele-level determination, and other more niche applications (e.g. novel allele/splice detection). |
immunoseq2airr | Convert Adaptive Biotech’s immunoSEQ format TCR data to the Adaptive Immune Receptor Repertoire-Community (AIRR-C) standard format. |
IMGTgeneDL | Automated downloading of TCR/IG sequences from IMGT/GENE-DB. |
genedb-releases | Banked snapshots of the entirety of IMGT/GENE-DB (i.e. both TCR and IG, all species/loci), to allow comparison between versions and reproduction of historical analyses. |
novel-tcr-alleles | Collated resource of published novel TCR alleles. |
airrc2hlaguessr | Convert AIRR-C format data into that required for HLAGuessr. |
Alternatively all of my repositories and contributions can be seen via my Github page.