Package Recipe 'bioconductor-mofa2'

recipe bioconductor-mofa2

Multi-Omics Factor Analysis v2

Homepage:: https://bioconductor.org/packages/3.20/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:

1.20.2-0, 1.16.0-0, 1.12.0-0, 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:

on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-basilisk >=1.22.0,<1.23.0a0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedarray >=0.36.0,<0.37.0a0
on bioconductor-hdf5array >=1.38.0,<1.39.0
on bioconductor-hdf5array >=1.38.0,<1.39.0a0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-rhdf5 >=2.54.1,<2.55.0a0
on r-base >=4.5,<4.6.0a0
on r-corrplot
on r-cowplot
on r-dplyr
on r-forcats
on r-ggplot2
on r-ggrepel
on r-magrittr
on r-pheatmap
on r-rcolorbrewer
on r-reshape2
on r-reticulate
on r-rtsne
on r-stringi
on r-tidyr
on r-uwot

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-mofa2

to add into an existing workspace instead, run:

pixi add bioconductor-mofa2

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-mofa2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mofa2

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-mofa2:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-mofa2/README.html)