Package: ClustIRR
Type: Package
Title: Clustering of immune receptor repertoires
Version: 1.6.0
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)
git_url: https://git.bioconductor.org/packages/ClustIRR
git_branch: RELEASE_3_21
git_last_commit: b44e437
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
Packaged: 2025-04-15 23:55:52 UTC; biocbuild
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 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:09:43 UTC; windows
Archs: x64
