Registration Open for Bioc2024 July 24-26


Stan implementation of BASiCS

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("BASiCStan")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An introduction to BASiCStan HTML R Script
Reference Manual PDF


biocViews Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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)
System Requirements GNU make
Bug Reports
See More
Suggests testthat (>= 3.0.0), knitr, rmarkdown
Linking To BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>=, RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BASiCStan_1.6.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) BASiCStan_1.6.0.tgz
macOS Binary (arm64) BASiCStan_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats