recipe bioconductor-combi

Compositional omics model based visual integration

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-combi/meta.yaml

This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.

package bioconductor-combi

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-phyloseq:

>=1.46.0,<1.47.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-alabama:

depends r-base:

>=4.3,<4.4.0a0

depends r-bb:

depends r-cobs:

depends r-dbi:

depends r-ggplot2:

depends r-matrix:

>=1.6.0

depends r-nleqslv:

depends r-reshape2:

depends r-tensor:

depends r-vegan:

requirements:

additional platforms:

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-combi

and update with::

   mamba update bioconductor-combi

To create a new environment, run:

mamba create --name myenvname bioconductor-combi

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-combi:<tag>

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

Download stats

Link to this page

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