MOFA

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MOFA (see replacement MOFA2).

Multi-Omics Factor Analysis (MOFA)


Bioconductor version: 3.9

Multi-Omics Factor Analysis: an unsupervised framework for the integration of multi-omics data sets.

Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle

Maintainer: Britta Velten <britta.velten at embl.de>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("MOFA")

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("MOFA")
Introduction to MOFA HTML R Script
MOFA: Application to a single-cell multi-omics data set HTML R Script
MOFA: applications to a multi-omics data set of CLL patients HTML R Script
MOFA: How to do assess model robustness and do model selection HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, DimensionReduction, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License LGPL-3 | file LICENSE
Depends R (>= 3.5)
Imports rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2, ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot, ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach, reticulate, grDevices, stats, utils
System Requirements Python (>=2.7.0), numpy, pandas, h5py, scipy, sklearn, mofapy
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Suggests knitr, MOFAdata
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Package Archives

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

Source Package MOFA_1.0.0.tar.gz
Windows Binary MOFA_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MOFA_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MOFA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MOFA
Bioc Package Browser https://code.bioconductor.org/browse/MOFA/
Package Short Url https://bioconductor.org/packages/MOFA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive