MOFA2

DOI: 10.18129/B9.bioc.MOFA2    

This is the development version of MOFA2; for the stable release version, see MOFA2.

Multi-Omics Factor Analysis v2

Bioconductor version: Development (3.14)

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.

Author: Ricard Argelaguet [aut] , Damien Arnol [aut] , Danila Bredikhin [aut] , Britta Velten [aut, cre]

Maintainer: Britta Velten <britta.velten at gmail.com>

Citation (from within R, enter citation("MOFA2")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MOFA2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MOFA2")

 

HTML R Script Downstream analysis: Overview
HTML R Script MEFISTO on simulated data (temporal)
HTML R Script MOFA2: How to train a model in R
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Bayesian, DimensionReduction, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.12 (R-4.0) (0.5 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 4.0)
Imports rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi
LinkingTo
Suggests knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix
SystemRequirements Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2
Enhances
URL https://biofam.github.io/MOFA2/index.html
BugReports https://github.com/bioFAM/MOFA2
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MOFA2_1.3.0.tar.gz
Windows Binary MOFA2_1.3.0.zip
macOS 10.13 (High Sierra) MOFA2_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MOFA2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MOFA2
Package Short Url https://bioconductor.org/packages/MOFA2/
Package Downloads Report Download Stats

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