recipe bioconductor-rtreemix

Rtreemix: Mutagenetic trees mixture models.

Homepage:

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

License:

LGPL

Recipe:

/bioconductor-rtreemix/meta.yaml

Links:

biotools: rtreemix, doi: 10.1093/bioinformatics/btn410

Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.

package bioconductor-rtreemix

versions:

1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.56.0-2,  1.56.0-1,  1.56.0-0,  1.54.0-0,  1.52.0-1, 

1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.56.0-2,  1.56.0-1,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-graph:

>=1.80.0,<1.81.0a0

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

depends r-hmisc:

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-rtreemix

and update with::

   mamba update bioconductor-rtreemix

To create a new environment, run:

mamba create --name myenvname bioconductor-rtreemix

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-rtreemix:<tag>

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

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