Resources
Here I’m slowly adding materials I created or co-created. Use them freely, with attribution :)
Datasets (Zenodo)
- Gene expression from canine cancers — quantified RNAseq data for samples from 418 dog patients with 14 cancer types (study)
- Canine antibody repertoire (protein) — 430k+ non-redundant variable domain sequences (heavy, kappa, lambda), from (study)
- Canine antibody repertoire (nucleotide) — 660k+ variable domain sequences (heavy, kappa, lambda), to be released with an upcoming study
Tools & Pipelines
- R package (coming) for immune repertoire analysis
- Nextflow pipeline (coming) for immune repertoire analysis
AI Models
- Antibody translation model — transformer for converting human/murine antibodies to canine “protein language” (study)
Fixes
- Docker image for XGDAG — unofficial containerized environment for the XGDAG, a gene prioritization graph neural network (GNN)
Guides & Tutorials
- IgBlast setup guide (coming) for non-model species
Intro to Science
Email me if you’d like to contribute! Planned: a guidebook for junior researchers: ambitious MSc students, beginning PhDs, and independent scientists, especially those with limited access to academic mentorship and training in reproducible science.