immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

Bioinformatics
Cédric R. WeberVictor Greiff

Abstract

B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis, such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, cluster...Continue Reading

References

May 27, 2015·Bioinformatics·Yana SafonovaJennie Lill
Nov 22, 2015·Genome Medicine·Gur Yaari, Steven H Kleinstein
Jun 22, 2017·Nature·Jacob GlanvilleMark M Davis
Sep 20, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Victor GreiffSai T Reddy
Nov 23, 2017·Frontiers in Immunology·Felix BredenThomas B Kepler

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Citations

Sep 9, 2020·Nature Biotechnology·Pierre BarennesEncarnita Mariotti-Ferrandiz
Sep 10, 2020·IScience·Lucia CsepregiSai T Reddy
Apr 15, 2021·Annual Review of Chemical and Biomolecular Engineering·Margarita PertsevaSai T Reddy

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Software Mentioned

- Quest
immuneSIM
HighV
R package
immuneSIM R
AbSim
IMGT
Quest

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