MOFA

DOI: 10.18129/B9.bioc.MOFA    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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 assess model robustness and do model selection
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, DimensionReduction, Software, Visualization
Version	1.6.2
In Bioconductor since	BioC 3.9 (R-3.6) (2 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
LinkingTo
Suggests	knitr, MOFAdata
SystemRequirements	Python (>=2.7.0), numpy, pandas, h5py, scipy, sklearn, mofapy
Enhances
URL
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	MOFA_1.6.2.tar.gz
Windows Binary	MOFA_1.6.2.zip
macOS 10.13 (High Sierra)	MOFA_1.6.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MOFA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MOFA
Package Short Url	https://bioconductor.org/packages/MOFA/
Package Downloads Report	Download Stats