recipe bioconductor-hopach

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-hopach/meta.yaml

Links:

biotools: hopach, doi: 10.1038/nmeth.3252

The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

package bioconductor-hopach

versions:

2.62.0-0,  2.60.0-0,  2.58.0-1,  2.58.0-0,  2.54.0-2,  2.54.0-1,  2.54.0-0,  2.52.0-0,  2.50.0-1, 

2.62.0-0,  2.60.0-0,  2.58.0-1,  2.58.0-0,  2.54.0-2,  2.54.0-1,  2.54.0-0,  2.52.0-0,  2.50.0-1,  2.50.0-0,  2.48.0-0,  2.46.0-0,  2.44.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

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-hopach

and update with::

   mamba update bioconductor-hopach

To create a new environment, run:

mamba create --name myenvname bioconductor-hopach

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-hopach:<tag>

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

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