BASiCStan

DOI: 10.18129/B9.bioc.BASiCStan  

Stan implementation of BASiCS

Bioconductor version: Release (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 outlook.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	An introduction to BASiCStan
PDF		Reference Manual
Text		NEWS

Details

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 (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests	testthat (>= 3.0.0), knitr, rmarkdown
SystemRequirements	GNU make
Enhances
URL	https://github.com/Alanocallaghan/BASiCStan
BugReports	https://github.com/Alanocallaghan/BASiCStan/issues
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	BASiCStan_1.0.0.tar.gz
Windows Binary	BASiCStan_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	BASiCStan_1.0.0.tgz
macOS Binary (arm64)	BASiCStan_1.0.0.tgz
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/
Package Downloads Report	Download Stats