Package: BASiCStan
Title: Stan implementation of BASiCS
Version: 1.15.0
Date: 2024-02-14
Authors@R: 
    c(
        person(
            given = "Alan",
            family = "O'Callaghan",
            role = c("aut", "cre"),
            email = "alan.ocallaghan@outlook.com"
        ),
        person(
            given = "Catalina",
            family = "Vallejos",
            role = c("aut")
        )
    )
Description: Provides an interface to infer the parameters of BASiCS
        using the variational inference (ADVI), Markov chain Monte
        Carlo (NUTS), and maximum a posteriori (BFGS) inference engines
        in the Stan programming language. BASiCS is a Bayesian
        hierarchical model that uses an adaptive Metropolis within
        Gibbs sampling scheme. Alternative inference methods provided
        by Stan may be preferable in some situations, for example for
        particularly large data or posterior distributions with
        difficult geometries.
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Biarch: true
Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1)
Imports: methods, glmGamPoi, scran, scuttle, stats, utils,
        SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0),
        RcppParallel (>= 5.0.1), rstantools (>= 2.1.1)
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
biocViews: ImmunoOncology, Normalization, Sequencing, RNASeq, Software,
        GeneExpression, Transcriptomics, SingleCell,
        DifferentialExpression, Bayesian, CellBiology
URL: https://github.com/Alanocallaghan/BASiCStan
BugReports: https://github.com/Alanocallaghan/BASiCStan/issues
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:52 UTC
RemoteUrl: https://github.com/bioc/BASiCStan
RemoteRef: HEAD
RemoteSha: 5f51c5f15123607e1198111955b04007e4474cf5
NeedsCompilation: yes
Packaged: 2026-05-30 09:36:39 UTC; root
Author: Alan O'Callaghan [aut, cre],
  Catalina Vallejos [aut]
Maintainer: Alan O'Callaghan <alan.ocallaghan@outlook.com>