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>

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

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
Links To Me
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)
Source Repository git clone https://git.bioconductor.org/packages/BASiCStan
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BASiCStan
Package Short Url https://bioconductor.org/packages/BASiCStan/
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