Package: BASiCStan 1.7.0

Alan OCallaghan

BASiCStan: Stan implementation of BASiCS

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.

Authors:Alan O'Callaghan [aut, cre], Catalina Vallejos [aut]

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BASiCStan.pdf |BASiCStan.html✨
BASiCStan/json (API)
NEWS

# Install 'BASiCStan' in R:

install.packages('BASiCStan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alanocallaghan/basicstan/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:BASiCStan-1.7.0(bioc 3.20)BASiCStan-1.6.0(bioc 3.19)

bioconductor-package

2 exports 0.71 score 153 dependencies

Last updated 2 months agofrom:ea995e970b

Exports:BASiCStan Stan2BASiCS

Dependencies:abind askpass assertthat backports base64enc BASiCS beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster bslib cachem callr checkmate cli cluster coda codetools colorspace colourpicker commonmark cowplot cpp11 crayon curl DelayedArray DelayedMatrixStats desc digest distributional dqrng edgeR evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggExtra ggplot2 glmGamPoi glue gridExtra gtable HDF5Array hexbin highr htmltools htmlwidgets httpuv httr igraph inline IRanges irlba isoband jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle limma locfit loo magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime miniUI munsell nlme numDeriv openssl pillar pkgbuild pkgconfig plyr posterior processx promises ps QuickJSR R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppHNSW RcppParallel reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown rstan rstantools rsvd S4Arrays S4Vectors sass ScaledMatrix scales scran scuttle shiny shinyjs SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats StanHeaders statmod stringi stringr SummarizedExperiment sys tensorA tibble tinytex UCSC.utils utf8 vctrs viridis viridisLite withr xfun xtable XVector yaml zlibbioc

An introduction to BASiCStan

Rendered fromBASiCStan.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2022-08-03
Started: 2021-11-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'BASiCStan' package.	BASiCStan-package
Stan implementation of BASiCS.	BASiCStan
Convert Stan fits to 'BASiCS_Chain' objects.	Stan2BASiCS