ImSpectR: R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data

Abstract

Abstract Summary An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions. Availability and implementation R-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR. Contact m.cordes@lumc.nl Supplementary information Supplementary data are available at Bioinformatics online.