BASiCStan
Stan implementation of BASiCS
Bioconductor version: Release (3.17)
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("BASiCStan")):
Installation
To install this package, start R (version "4.3") 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")| An introduction to BASiCStan | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1 year) |
| 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) |
| 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) |
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown |
| System Requirements | GNU make |
| Enhances | |
| URL | https://github.com/Alanocallaghan/BASiCStan |
| Bug Reports | https://github.com/Alanocallaghan/BASiCStan/issues |
See More
| 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_1.2.0.tar.gz |
| Windows Binary | BASiCStan_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | BASiCStan_1.2.0.tgz |
| macOS Binary (arm64) | BASiCStan_1.2.0.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 |