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Bioconductor - BASiCStan

BASiCStan

This is the released version of BASiCStan; for the devel version, see BASiCStan.

Stan implementation of BASiCS

Bioconductor version: Release (3.21)

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 "4.5") and enter:


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

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")
Details biocViews Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.10.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 Package Archives

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

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