Package: BASiCStan
Title: Stan implementation of BASiCS
Version: 1.14.1
Date: 2026-06-30
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)
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/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/BASiCStan
git_branch: RELEASE_3_23
git_last_commit: 395211e
git_last_commit_date: 2026-06-30
Repository: Bioconductor 3.23
Date/Publication: 2026-07-02
NeedsCompilation: yes
Packaged: 2026-07-02 20:33:52 UTC; biocbuild
Author: Alan O'Callaghan [aut, cre],
  Catalina Vallejos [aut]
Maintainer: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Built: R 4.6.1; x86_64-pc-linux-gnu; 2026-08-13 20:02:30 UTC; unix
