recipe bioconductor-bhc

Bayesian Hierarchical Clustering

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/BHC.html

License:

GPL-3

Recipe:

/bioconductor-bhc/meta.yaml

Links:

biotools: bhc, doi: 10.1186/1471-2105-10-242

The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.

package bioconductor-bhc

versions:

1.54.0-0,  1.52.0-0,  1.50.0-2,  1.50.0-1,  1.50.0-0,  1.46.0-2,  1.46.0-1,  1.46.0-0,  1.44.0-0, 

1.54.0-0,  1.52.0-0,  1.50.0-2,  1.50.0-1,  1.50.0-0,  1.46.0-2,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

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-bhc

and update with::

   mamba update bioconductor-bhc

To create a new environment, run:

mamba create --name myenvname bioconductor-bhc

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 quay.io/biocontainers/bioconductor-bhc:<tag>

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

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