DESCRIPTION

Package: ClustIRR
Type: Package
Title: Clustering of immune receptor repertoires
Version: 1.5.9
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
LazyData: false
Depends:
    R (>= 4.4.0)
Imports:
    blaster,
    future,
    future.apply,
    grDevices,
    igraph,
    methods,
    pwalign,
    Rcpp (>= 0.12.0),
    RcppParallel (>= 5.0.1),
    reshape2,
    rstan (>= 2.18.1),
    rstantools (>= 2.4.0),
    stats,
    stringdist,
    utils,
    posterior,
    visNetwork
Suggests:
    BiocStyle,
    knitr,
    testthat,
    ggplot2,
    ggrepel,
    patchwork
Encoding: UTF-8
NeedsCompilation: no
biocViews: Clustering, ImmunoOncology, SingleCell, Software, Classification
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)
SystemRequirements: GNU make