Package: IgGeneUsage Type: Package Title: Differential gene usage in immune repertoires Version: 1.27.0 Authors@R: person(given = "Simo", family = "Kitanovski", role = c("aut", "cre"), email = "simo.kitanovski@uni-due.de") Description: Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing. License: MIT + file LICENSE Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) SystemRequirements: GNU make Encoding: UTF-8 LazyData: false NeedsCompilation: yes biocViews: DifferentialExpression, Regression, Genetics, Bayesian, BiomedicalInformatics, ImmunoOncology, MathematicalBiology BugReports: https://github.com/snaketron/IgGeneUsage/issues URL: https://github.com/snaketron/IgGeneUsage RoxygenNote: 6.1.1 VignetteBuilder: knitr Biarch: true Config/pak/sysreqs: make libicu-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:50:40 UTC RemoteUrl: https://github.com/bioc/IgGeneUsage RemoteRef: HEAD RemoteSha: a368ba5119a7d9b7d7333ee15ad1ad3844ed0372 Packaged: 2026-07-04 11:00:29 UTC; root Author: Simo Kitanovski [aut, cre] Maintainer: Simo Kitanovski