Package: IgGeneUsage
Type: Package
Title: Differential gene usage in immune repertoires
Version: 1.25.0
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: 2025-10-29 14:53:29 UTC
RemoteUrl: https://github.com/bioc/IgGeneUsage
RemoteRef: HEAD
RemoteSha: 03134f129e51a8a1bd3f72a6cd7e2fe73c906048
Packaged: 2025-10-30 06:47:48 UTC; root
Author: Simo Kitanovski [aut, cre]
Maintainer: Simo Kitanovski <simo.kitanovski@uni-due.de>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 06:54:44 UTC; windows
Archs: x64
