recipe bioconductor-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.

package bioconductor-basicstan

(downloads) docker_bioconductor-basicstan



depends bioconductor-basics:


depends bioconductor-basics:


depends bioconductor-glmgampoi:


depends bioconductor-glmgampoi:


depends bioconductor-scran:


depends bioconductor-scran:


depends bioconductor-scuttle:


depends bioconductor-scuttle:


depends bioconductor-singlecellexperiment:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-summarizedexperiment:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-bh:


depends r-rcpp:


depends r-rcppeigen:


depends r-rcppparallel:


depends r-rstan:


depends r-rstantools:


depends r-stanheaders:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-basicstan

and update with::

   mamba update bioconductor-basicstan

To create a new environment, run:

mamba create --name myenvname bioconductor-basicstan

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-basicstan/tags`_ for valid values for ``<tag>``)

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