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.