MOFA2

This is the released version of MOFA2; for the devel version, see MOFA2.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Multi-Omics Factor Analysis v2

Bioconductor version: Release (3.23)

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, visualisation, imputation etc are available.

Author: Ricard Argelaguet [aut, cre] ORCID: 0000-0003-3199-3722 , Damien Arnol [aut] ORCID: 0000-0003-2462-534X , Danila Bredikhin [aut] ORCID: 0000-0001-8089-6983 , Britta Velten [aut] ORCID: 0000-0002-8397-3515

Maintainer: Ricard Argelaguet <ricard.argelaguet at gmail.com>

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

Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Britta Velten. MOFA2: Multi-Omics Factor Analysis v2. doi:10.18129/B9.bioc.MOFA2, R package version 1.22.1, https://bioconductor.org/packages/MOFA2.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, DimensionReduction, Software, Visualization
Version	1.22.1
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	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
System Requirements	Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2
URL	https://biofam.github.io/MOFA2/index.html
Bug Reports	https://github.com/bioFAM/MOFA2

Suggests	knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown
Linking To
Enhances
Depends On Me
Imports Me	RFLOMICS
Suggests Me	HoloFoodR, OMA, SUMO, tidyexposomics
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MOFA2_1.22.1.tar.gz
Windows Binary (x86_64)	MOFA2_1.22.1.zip
macOS Binary (big-sur-x86_64)	MOFA2_1.22.1.tgz
macOS Binary (sonoma-arm64)	MOFA2_1.22.1.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
Old Source Packages for BioC 3.23	Source Archive