sumrep

sumrep is an R package to facilitate the analysis of adaptive immune receptor repertoire sequencing (AIRR-seq) datasets. These datasets contain DNA sequences coding for antigen receptors of B and T cells. These are generated through a complex recombination process and further diversified by affinity maturation in B cells. The complexity of AIRR-seq datasets makes their analysis challenging.

The sumrep package provides a range of functions to summarize and compare repertoires efficiently. It can be used for model validation by assessing the ability of different summaries to differentiate between datasets based on various covariates, such as donor, timepoint, and cell type, in both BCR and TCR repertoires.

The authors found that specific summaries, particularly those related to deletion and insertion lengths resulting from V(D)J recombination, are more effective at discriminating between repertoires than summaries describing the amino acid composition of the CDR3 region.

Additionally, the study reveals that while state-of-the-art generative models perform well in recapitulating gene usage and recombination statistics of experimental repertoires, they have difficulty capturing many physiochemical properties of real repertoires.