Software

2022

CompAIRR | Bioinformatics | github
CompAIRR is a command line tool for comparing two sets of adaptive immune receptor repertoires and compute their overlap; identifying which sequences are present in which repertoires; and clustering the sequences in a repertoire set.

2021

Igeminio | mAbs | github
Igeminio is a machine learning generative model for the exploration of high-affinity antibody sequences with desired developability properties.

Absolut! | Website | Nature Comp. Sci. | github
Absolut! is a framework (software and database) for the large-scale generation of antibody-antigen complexes, as the basis for ML benchmarking.

immuneML | Website | bioRxiv | github
immuneML is a machine learning platform for disease diagnostics based on interrogation of the adaptive immune system that allows both novices and experts to perform immune repertoire analyses in an efficient and reproducible manner.

2020

ImmuneSIM | Article | Github | CRAN
immuneSIM is a simulation package for in silico generating human and mouse B- and T-cell repertoires with user-defined properties to provide the user with custom native or aberrant immune receptor sequence repertoires to benchmark their repertoire analysis tools.

ImmuneREF | Under development

2019

Paratope-Epitope prediction | Preprint | Github

ImmunoProbs | Github
ImmunoProbs is a Python wrapper for the IGoR package (Marcou, Mora & Walczak, Nature Communications, 2018). ImmunoProbs with all its dependencies is also available via Docker.