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BASiCStan

This is the development version of BASiCStan; for the stable release version, see BASiCStan.

Stan implementation of BASiCS


Bioconductor version: Development (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 outlook.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BASiCStan")

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

Documentation

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

browseVignettes("BASiCStan")
An introduction to BASiCStan HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.5.1
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
URL https://github.com/Alanocallaghan/BASiCStan
Bug Reports https://github.com/Alanocallaghan/BASiCStan/issues
See More
Suggests testthat (>= 3.0.0), knitr, rmarkdown
Linking To 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)
Enhances
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Package Archives

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

Source Package BASiCStan_1.5.1.tar.gz
Windows Binary BASiCStan_1.5.1.zip (64-bit only)
macOS Binary (x86_64) BASiCStan_1.5.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/BASiCStan
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BASiCStan
Bioc Package Browser https://code.bioconductor.org/browse/BASiCStan/
Package Short Url https://bioconductor.org/packages/BASiCStan/
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