Package: ClustIRR
Type: Package
Title: Clustering of immune receptor repertoires
Version: 1.8.0
Authors@R: c(
    person("Simo", "Kitanovski", email = "simokitanovski@gmail.com", 
    role = c("aut", "cre"), comment=c(ORCID="0000-0003-2909-5376")),
    person("Kai", "Wollek", email = "kai.wollek@uni-duisburg-essen.de", 
    role = c("aut"), comment=c(ORCID="0009-0008-5941-9160")))
Description: ClustIRR analyzes repertoires of B- and T-cell receptors.
        It starts by identifying communities of immune receptors with
        similar specificities, based on the sequences of their
        complementarity-determining regions (CDRs). Next, it employs a
        Bayesian probabilistic models to quantify differential
        community occupancy (DCO) between repertoires, allowing the
        identification of expanding or contracting communities in
        response to e.g. infection or cancer treatment.
License: GPL-3 + file LICENSE
Depends: R (>= 4.3.0)
Imports: blaster, future, future.apply, grDevices, igraph, methods,
        Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
        2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils,
        posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales
Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
SystemRequirements: GNU make
Encoding: UTF-8
LazyData: false
NeedsCompilation: yes
biocViews: Clustering, ImmunoOncology, SingleCell, Software,
        Classification, Bayesian, BiomedicalInformatics,
        ImmunoOncology, MathematicalBiology
RoxygenNote: 7.2.3
VignetteBuilder: knitr
URL: https://github.com/snaketron/ClustIRR
BugReports: https://github.com/snaketron/ClustIRR/issues
Biarch: true
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)
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        make libicu-dev libxml2-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:25:33 UTC
RemoteUrl: https://github.com/bioc/ClustIRR
RemoteRef: RELEASE_3_22
RemoteSha: 0b886ef8ad78ca57a95ba44f1ab5be632399716b
Packaged: 2025-11-11 13:46:24 UTC; root
Author: Simo Kitanovski [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2909-5376>),
  Kai Wollek [aut] (ORCID: <https://orcid.org/0009-0008-5941-9160>)
Maintainer: Simo Kitanovski <simokitanovski@gmail.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:52:51 UTC; windows
Archs: x64
