recipe bioconductor-mofa2

Multi-Omics Factor Analysis v2

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/MOFA2.html

License:

file LICENSE

Recipe:

/bioconductor-mofa2/meta.yaml

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

package bioconductor-mofa2

versions:

1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.1-0,  1.0.0-1

depends bioconductor-basilisk:

>=1.12.0,<1.13.0

depends bioconductor-delayedarray:

>=0.26.0,<0.27.0

depends bioconductor-hdf5array:

>=1.28.0,<1.29.0

depends bioconductor-rhdf5:

>=2.44.0,<2.45.0

depends r-base:

>=4.3,<4.4.0a0

depends r-corrplot:

depends r-cowplot:

depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-ggrepel:

depends r-magrittr:

depends r-pheatmap:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-reticulate:

depends r-rtsne:

depends r-stringi:

depends r-tidyr:

depends r-uwot:

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-mofa2

and update with::

   mamba update bioconductor-mofa2

To create a new environment, run:

mamba create --name myenvname bioconductor-mofa2

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-mofa2:<tag>

(see `bioconductor-mofa2/tags`_ for valid values for ``<tag>``)

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Link to this page

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