DOI: 10.18129/B9.bioc.BASiCStan  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BASiCStan.

Stan implementation of BASiCS

Bioconductor version: 3.16

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.

Author: Alan O'Callaghan [aut, cre], Catalina Vallejos [aut]

Maintainer: Alan O'Callaghan <alan.ocallaghan at>

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biocViews Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
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 (>=, RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests testthat (>= 3.0.0), knitr, rmarkdown
SystemRequirements GNU make
Depends On Me
Imports Me
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